Mutant pores

ABSTRACT

The invention relates to mutant forms of CsgG. The invention also relates to analyte detection and characterisation using CsgG.

This Application is a national stage filing under 35 U.S.C. 371 ofInternational Patent Application Serial No. PCT/GB2017/050571, filedMar. 2, 2017, entitled “MUTANT PORES” which claims foreign priorityunder 35 U.S.C. § 119(a)-(d) or 35 U.S.C. § 365(b) to Britishapplication number GB 1603656.8, filed Mar. 2, 2016, British applicationnumber GB 1603657.6, filed Mar. 2, 2016, and British application numberGB 1603658.4, filed Mar. 2, 2016. The contents of these applications areincorporated herein by reference in their entireties.

FIELD OF THE INVENTION Background of the Invention

Nanopore sensing is an approach to sensing that relies on theobservation of individual binding or interaction events between analytemolecules and a receptor. Nanopore sensors can be created by placing asingle pore of nanometer dimensions in an insulating membrane andmeasuring voltage-driven ionic transport through the pore in thepresence of analyte molecules. The identity of an analyte is revealedthrough its distinctive current signature, notably the duration andextent of current block and the variance of current levels. Suchnanopore sensors are commercially available, such as the MinION™ devicesold by Oxford Nanopore Technologies Ltd, comprising an array ofnanopores integrated with an electronic chip.

There is currently a need for rapid and cheap nucleic acid (e.g. DNA orRNA) sequencing technologies across a wide range of applications.Existing technologies are slow and expensive mainly because they rely onamplification techniques to produce large volumes of nucleic acid andrequire a high quantity of specialist fluorescent chemicals for signaldetection. Nanopore sensing has the potential to provide rapid and cheapnucleic acid sequencing by reducing the quantity of nucleotide andreagents required.

Two of the essential components of sequencing nucleic acids usingnanopore sensing are (1) the control of nucleic acid movement throughthe pore and (2) the discrimination of nucleotides as the nucleic acidpolymer is moved through the pore. In the past, to achieve nucleotidediscrimination the nucleic acid has been passed through a mutant ofhemolysin. This has provided current signatures that have been shown tobe sequence dependent. It has also been shown that a large number ofnucleotides contribute to the observed current when a hemolysin pore isused, making a direct relationship between observed current andpolynucleotide challenging.

While the current range for nucleotide discrimination has been improvedthrough mutation of the hemolysin pore, a sequencing system would havehigher performance if the current differences between nucleotides couldbe improved further. In addition, it has been observed that when thenucleic acids are moved through a pore, some current states show highvariance. It has also been shown that some mutant hemolysin poresexhibit higher variance than others. While the variance of these statesmay contain sequence specific information, it is desirable to producepores that have low variance to simplify the system. It is alsodesirable to reduce the number of nucleotides that contribute to theobserved current.

SUMMARY OF THE INVENTION

The inventors have surprisingly demonstrated that CsgG and novel mutantsthereof may be used to characterise analytes, such as polynucleotides.The invention concerns mutant CsgG monomers. The inventors havesurprisingly demonstrated that pores comprising the novel mutantmonomers have an enhanced ability to estimate the characteristics ofanalytes, such as the sequence of polynucleotides. The inventors havemade mutant pores that surprisingly provide more consistent movement ofa target polynucleotide with respect to, such as through, the pores. Theinventors have made mutant pores surprisingly display improvedcharacterisation accuracy. In particular, the mutant pores made by theinventors surprisingly display an increased current range, which makesit easier to discriminate between different nucleotides, and a reducedvariance of states, which increases the signal-to-noise ratio. Inaddition, the mutant pores surprisingly capture nucleotides andpolynucleotides more easily.

All amino-acid substitutions, deletions and/or additions disclosedherein are with reference to a mutant CsgG monomer comprising a variantof the sequence shown in SEQ ID NO: 2, unless stated to the contrary.

Reference to a mutant CsgG monomer comprising a variant of the sequenceshown in SEQ ID NO: 2 encompasses mutant CsgG monomers comprisingvariants of sequences as set out in the further SEQ ID NOS as disclosedbelow. Amino-acid substitutions, deletions and/or additions may be madeto CsgG monomers comprising a variant of the sequence other than shownin SEQ ID NO:2 that are equivalent to those substitutions, deletionsand/or additions disclosed herein with reference to a mutant CsgGmonomer comprising a variant of the sequence shown in SEQ ID NO:2.

A mutant monomer may be considered as an isolated monomer.

In particular, the invention concerns mutant CsgG monomers in which thearginine (R) at position 192 has been substituted with aspartic acid(D), glutamine (Q), phenylalanine (F), serine (S) or threonine (T). Theinventors have surprisingly demonstrated that such monomers, and inparticular a monomer comprising a R192D substitution, are much easier toexpress than monomers without a substitution at position 192. Anincreased yield is obtained when the CsgG monomer comprises thismutation.

The mutatnt csgG monomer may be:

-   -   a mutant CsgG monomer comprising a variant of the sequence shown        in SEQ ID NO: 2 which comprises R97W;    -   a mutant CsgG monomer which comprises (a) R192D; (b) R97W/Y        and/or R93W/Y, preferably R97W, R93W or R93Y and R97Y; (c)        K94Q/N; (d) G103K/R and/or T104K/R; and/or (e) F191T, deletion        of V105, A106 and I107 and/or deletion of F193, I194, D195,        Y196, Q197, R198 and L199.

The mutant CsgG monomer preferably further comprises Y51A and F56Q.

Particular mutant CsgG monomers comprise variants of the sequence shownin SEQ ID NO: 2 that comprise the following mutations:

(1) Y51A, F56Q and R192D;

(2) Y51A, F56Q and R97W.

(3) Y51A, F56Q, R192D and R97W;

(4) Y51A, F56Q, R192D and R93W;

(5) Y51A, F56Q, R192D, R93Y and R97Y; or

(6) Y51A, F56Q, R192D and R93W.

(7) the mutations of any one of (1)-(6) and:

-   -   (a) deletion of V105, A106 and I107.    -   (b) K94Q or K94N;    -   (c) deletion of D195, Y196, Q197, R198 and L199 or deletion of        F193, I194, D195, Y196, Q197, R198 and L199; and/or    -   (d) F191T.

(8) the mutations of any one of (1)-(6) and:

-   -   (i) K94Q and deletion of V105, A106 and I107;    -   (ii) K94N and deletion of V105, A106 and I107;    -   (iii) F191T and deletion of V105, A106 and I107;    -   (iv) K94Q and F191T;    -   (v) K94N and F191T;    -   (vi) K94Q, F191T and deletion of V105, A106 and I107; or    -   (vii) K94N, F191T and deletion of V105, A106 and I107.

(9) the mutations of any one of (1)-(8) and:

-   -   T104K or T104R;    -   L90R;    -   N91R;    -   I95R;    -   A99R;    -   E101K, E101N, E101Q, E101T or E101H;    -   E44N or E44Q; and/or    -   Q42K.

The invention also provides:

-   -   a construct comprising two or more covalently attached CsgG        monomers, wherein at least one of the monomers is a mutant        monomer of the invention;    -   a polynucleotide which encodes a mutant monomer of the invention        or a construct of the invention;    -   a homo-oligomeric pore derived from CsgG comprising identical        mutant monomers of the invention or identical constructs of the        invention;    -   a hetero-oligomeric pore derived from CsgG comprising at least        one mutant monomer of the invention or at least one construct of        the invention;    -   a method for determining the presence, absence or one or more        characteristics of a target analyte, comprising:

(a) contacting the target analyte with a pore of the invention such thatthe target analyte moves with respect to the pore; and

(b) taking one or more measurements as the analyte moves with respect tothe pore and thereby determining the presence, absence or one or morecharacteristics of the analyte;

-   -   a method of forming a sensor for characterising a target        polynucleotide, comprising forming a complex between a pore of        the invention and a polynucleotide binding protein and thereby        forming a sensor for characterising the target polynucleotide;    -   a sensor for characterising a target polynucleotide, comprising        a complex between a pore of the invention and a polynucleotide        binding protein;    -   use of a pore of the invention to determine the presence,        absence or one or more characteristics of a target analyte;    -   a kit for characterising a target analyte comprising (a) a pore        of the invention and (b) the components of a membrane;    -   an apparatus for characterising target analytes in a sample,        comprising (a) a plurality of a pores of the invention and (b) a        plurality of membranes;    -   a method of characterising a target polynucleotide, comprising:

a) contacting the polynucleotide with a pore of the invention, apolymerase and labelled nucleotides such that phosphate labelled speciesare sequentially added to the target polynucleotide by the polymerase,wherein the phosphate species contain a label specific for eachnucleotide; and

b) detecting the phosphate labelled species using the pore and therebycharacterising the polynucleotide; and

-   -   a method of producing a mutant monomer of the invention or a        construct of the invention, comprising expressing a        polynucleotide of the invention in a suitable host cell and        thereby producing a mutant monomer of the invention or a        construct.

DESCRIPTION OF THE FIGURES

FIG. 1: Illustrates CsgG from E. coli.

FIG. 2: Illustrates the dimensions of CsgG.

FIG. 3: Illustrates single G translocation at 10 Å/ns. There is a largebarrier for entry of guanine into F56 ring in CsgG-Eco. *=G enters F56ring. A=G stops interacting with 56 ring. B=G stops interacting with 55ring. C=G stops interacting with 51 ring.

FIG. 4: Illustrates ssDNA translocation at 100 Å/ns. A larger force isrequired to pull the DNA through the constriction for CsgG-Eco.

FIG. 5: Illustrates ss DNA translocation at 10 Å/ns. CsgG-F56A-N55S andCsG-F56A-N55S-Y51A mutants both have a lower barrier for ssDNAtranslocation.

FIGS. 6 to 8: Mutant pores showing increased range compared withwild-type (WT).

FIGS. 9 and 10: Mutant pores showing increased throughput compared withwild-type (WT).

FIGS. 11 and 12: Mutant pore showing increased insertion compared withwild-type (WT).

FIG. 13: shows the DNA construct X used in Example 2. The regionlabelled 1 corresponded to 30 SpC3 spacers. The region labelled 2corresponded to SEQ ID NO: 42. The region labelled 3 corresponded tofour iSp18 spacers. The region labelled 4 corresponded to SEQ ID NO: 43.The section labelled 5 corresponded to four 5-nitroindoles. The regionlabelled 6 corresponded to SEQ ID NO: 44. The region labelled 7corresponded to SEQ ID NO: 45. The region labelled 8 corresponded to SEQID NO: 46 which had four iSp18 spacers (the region labelled 9) attachedat the 3′ end of SEQ ID NO: 46. At the opposite end of the iSp18 spacerswas a 3′ cholesterol tether (labelled 10). The region labelled 11corresponded to four SpC3 spacers.

FIG. 14: shows an example chromatography trace of Strep trap (GEHealthcare) purification of CsgG protein (x-axis label=elution volume(mL), Y-axis label=Absorbance (mAu)). The sample was loaded in 25 mMTris, 150 mM NaCl, 2 mM EDTA, 0.01% DDM and eluted with 10 mMdesthiobiotin. The elution peak in which CsgG protein eluted is labelledas E1.

FIG. 15: shows an example of a typical SDS-PAGE visualisation of CsgGprotein after the initial strep purification. A 4-20% TGX Gel (Bio Rad)was run at 300 V for 22 minutes in 1×TGS buffer. The gel was stainedwith Sypro Ruby stain. Lanes 1-3 show the main elution peak (labelled E1in FIG. 14) which contained CsgG protein as indicated by the arrow.Lanes 4-6 corresponded to elution fractions of the tail of the mainelution peak (labelled E1 in FIG. 14) which contained contaminents. Mshows the molecular weight marker used which was a Novex Sharp Unstained(unit=kD).

FIG. 16: Shows an example of a size exclusion chromatogram (SEC) of CsgGprotein (120 mL S200 GE healthcare, x-axis label=elution volume (mL),y-axis label=absorbance (mAu)). The SEC was carried out after streppurification and heating the protein sample. The running buffer for SECwas 25 mM Tris, 150 mM NaCl, 2 mM EDTA, 0.01% DDM, 0.1% SDS, pH 8.0 andthe column was run at 1 mL/minute rate. The trace labelled X showsabsorbance at 220 nm and the trace labelled Y shows absorbance at 280nm. The peak labelled with a star was collected.

FIG. 17: shows an example of a typical SDS-PAGE visualisation of CsgGprotein after SEC. A 4-20% TGX Gel (Bio Rad) was run at 300V for 22minutes in 1×TGS buffer and the gel was stained with Sypro Ruby stain.Lane 1 shows CsgG protein sample after strep purification and heatingbut before SEC. Lanes 2-8 show fractions collected across the peakrunning approximately 48 mL 60 mL of FIG. 16 (mid peak=55 mL) andlabelled with a star in FIG. 16. M shows the molecular weight markerused which was a Novex Sharp Unstained (unit=kD). The bar correspondingto the CsgG-Eco pore is indicated by an arrow.

FIGS. 18 to 24: Mutant pores showing increased range compared withwild-type (WT).

FIGS. 25 to 30: Mutant pores showing increased range compared withwild-type (WT).

FIG. 31 shows snap shots of the enzyme (T4 Dda-(E94C/C109A/C136A/A360C)(SEQ ID NO: 24 with mutations E94C/C109A/C136A/A360C and then(ΔM1)G1G2)) on top of the pore (CsgG-Eco-(Y51T/F56Q)-StrepII(C))9 (SEQID NO: 2 with mutations Y51T/F56Q where StrepII(C) is SEQ ID NO: 47 andis attached at the C-terminus pore mutant No. 20)) taken at 0 and 20 nsduring the simulations (Runs 1 to 3).

FIG. 32 shows snap shots of the enzyme (T4 Dda-(E94C/C109A/C136A/A360C)(SEQ ID NO: 24 with mutations E94C/C109A/C136A/A360C and then(ΔM1)G1G2)) on top of the pore (CsgG-Eco-(Y51T/F56Q)-StrepII(C))9 (SEQID NO: 2 with mutations Y51T/F56Q where StrepII(C) is SEQ ID NO: 47 andis attached at the C-terminus pore mutant No. 20)) taken at 30 and 40 nsduring the simulations (Runs 1 to 3).

FIG. 33 shows a snap shot of the enzyme (T4 Dda(E94C/F98W/C109A/C136A/K194L/A360C) (SEQ ID NO: 24 with mutationsE94C/F98W/C109A/C136A/K194L/A360C and then (ΔM1)G1G2) on top of the poreCsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus pore mutant No. 26) taken during the simulations described inExample 5.

FIG. 34 shows two ten second screen shots of current traces showingtranslocation of DNA (SEQ ID NO: 51) through MspA mutantx=MspA-((Del-L74/G75/D118/L119)D56F/E59R/L88N/D90N/D91N/Q126R/D134R/E139K)8(SEQ ID NO: 50 with mutations D56F/E59R/L88N/D90N/D91N/Q126R/D134R/E139Kand deletion of the amino acids L74/G75/D118/L119) without the controlof an enzyme.

FIG. 35 shows two ten second screen shots of current traces showingtranslocation of DNA (SEQ ID NO: 51) throughCsgG-Eco-(Y51A/F56Q/R97W/R192D-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W/R192D where StrepII(C) is SEQ ID NO: 47 and is attachedat the C-terminus) without the control of an enzyme.

FIG. 36 shows two ten second screen shots of current traces showingtranslocation of DNA (SEQ ID NO: 51) throughCsgG-Eco-(Y51A/F56Q/R97W/E101S/R192D-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/R97W/E101S/R192D where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus) without the control of an enzyme.

FIG. 37 shows an overlay of two gel filtration chromatograms (120 mlS200 column) of the CsgG mutants pores A)CsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) and B) CsgG-Eco-(Y51A/F56Q/R97W/R192D)-StrepII(C))9 (SEQ IDNO: 2 with mutations Y51A/F56Q/R97W/R192D where StrepII(C) is SEQ ID NO:47 and is attached at the C-terminus). Absorbance at A280 forCsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 is labelled A and forCsgG-Eco-(Y51A/F56Q/R97W/R192D)-StrepII(C))9 is labelled B. Bothconstructs were grown in 500 ml cultures. Expression and purification ofboth proteins were carried out using exactly the same protocol and samevolumes were loaded onto the column. Running Buffer was 25 mM Tris, 150mM NaCl, 2 mM EDTA, 0.01% DDM, 0.1% SDS pH8. The fractional delay withCsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 pore was due to differentconnection configuration used on AKTA Purifier 10. The difference in theabsorbance values indicated the amount of proteins expressed with higherabsorbance values indicating higher amounts of expressed protein.

FIG. 38 shows SDS-PAGE analysis of CsgG nanopores. Lanes A-C containedCsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9, lanes D-F containedCsgG-Eco-(Y51A/F56Q/R97W/R192D)-StrepII(C))9 and lane M contained themolecular weight marker. The two pores were expressed and purified usingexactly the same protocol. The pores were subjected to electrophoresison a 4-20% TGX gel (Bio rad cat #5671093) in TGS buffer at 300 V for 22minutes. The gel was visualised with Sypro Ruby stain (Life Technologiescat#S1200). The same volumes from each pore sample were loaded on thegel to compare the amount of proteins obtained after purification—lanesA and D contained 5 uL, lanes B and E contained 10 uL and lanes C and Fcontained 15 uL.

FIG. 39 shows the basecall accuracy of eight CsgG mutant pores comparedto the basecall accuracy of a baseline pore, mutant 28(CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9). The deletion of D195-L199(Mutant A), F193-L199 (Mutant B) or V105-I107 (Mutant D), or thesubstitution of F191T (Mutant C) results in a further improvement inaccuracy in addition to the improvement in accuracy resulting from theR97W and R192D substitutions in mutant 28. The effect on basecallaccuracy of deleting V105-I107 was also tested in a mutant porecontaining an additional K94Q mutation (Mutant E) and an improvement inaccuracy compared to baseline mutant 28 was still observed. Introducinga R93W mutation (Mutant F) or both R93Y and R97W mutations (Mutant H)instead of a R97W mutation (baseline mutant 28) increased the basecallaccuracy. Deleting D195-L199 in addition to R93W (Mutant G) resulted inan enhancement of basecall accuracy.

FIG. 40 shows the template speed distribution (A) and the templateaccuracy distribution (B) of the baseline mutant 28CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9 and Mutant D which comprises anadditional deletion of V105-I107. A template DNA was prepared and passedthrough the mutant pores as described in the Examples. The templatespeed and accuracy were determined as described in the Examples. FIG.40A shows that the speed distribution was tighter when Mutant D was usedcompared to the baseline mutant. FIG. 40B shows that mutant D has atighter distribution of template accuracy compared to the baselinemutant.

FIG. 41 displays an example “squiggle” that shows the “noisy” pore errormode exhibited by baseline mutant 28CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9. The top panel of FIG. 41 showsthe difference in flow of current through the pore during the “good” and“noisy” pore states. The bottom panel of FIG. 41 shows an expanded viewof the transition from “good” state to “noisy” state.

FIG. 42 shows the reduction in noisy pore state of mutant pores havingthe same sequence as the baseline mutant 28, which containsY51A/F56Q/R97W/R192D mutations, with an additional K94N mutation (MutantI) or an additional K94Q mutation (Mutant J) when compared to baselinemutant 28, averaged over at least 5 runs.

FIG. 43 illustrates the structure of the template strand having anadapter ligated to each end thereof. The adapter has a T4 Dda helicaseenzyme prebound thereto. The sequences of the various parts of theadaptor used in the Examples are shown in SEQ ID NOs: 52 to 55.

FIG. 44 shows the median time between Thrombin Binding Aptamer (TBA)events for mutant CsgG nanopores comprising one of the followingsubstitutions: Q42K (Mutant K), E44N (Mutant L), E44Q (Mutant M), L90R(Mutant N), N91R (Mutant O), I95R (Mutant P), A99R (Mutant Q), E101H(Mutant R), E101K (Mutant S), E101N (Mutant T), E101Q (Mutant U), E101T(Mutant V) and Q114K (Mutant W). The median time was significantlyreduced compared to the baseline pore comprising the mutationsY51A/F56Q/K94Q/R97W/R192D-del(V105-I107) (Baseline mutant E), all ofwhich are also included in each of the 13 mutants tested. FIG. 44 showsthat each of the Q42K, E44N, E44Q, L90R, N91R, I95R, A99R, E101H, E101K,E101N, E101Q, E101T and Q114K substitutions increase template DNAcapture rates.

FIG. 45 shows sequence alignments of the 21 CsgG homologuescorresponding to SEQ ID Nos 2, 5, 6, 7, 27, 28, 29, 30, 32, 36, 3, 35,31, 40, 33, 34, 37, 39, 38, 41 and 4

FIG. 46 shows the same relative sequence alignments as FIG. 45 withpredicted alpha helical secondary structure regions additionally shaded.

FIG. 47 shows the same relative sequence alignments as FIG. 45 withpredicted beta sheet secondary structure regions additionally shaded.

FIG. 48 shows two examples of raw electrical data for poreAQ andpore97W.

DESCRIPTION OF THE SEQUENCE LISTING

SEQ ID NO: 1 shows the codon optimised polynucleotide sequence encodingthe wild-type CsgG monomer from Escherchia coli Str. K-12 substr.MC4100. This monomer lacks the signal sequence.

SEQ ID NO: 2 shows the amino acid sequence of the mature form of thewild-type CsgG monomer from Escherchia coli Str. K-12 substr. MC4100.This monomer lacks the signal sequence. The abbreviation used for thisCsgG=CsgG-Eco.

SEQ ID NO: 3 shows the amino acid sequence of YP_001453594.1: 1-248 ofhypothetical protein CKO_02032 [Citrobacter koseri ATCC BAA-895], whichis 99% identical to SEQ ID NO: 2.

SEQ ID NO: 4 shows the amino acid sequence of WP_001787128.1: 16-238 ofcurli production assembly/transport component CsgG, partial [Salmonellaenterica], which is 98% to SEQ ID NO: 2.

SEQ ID NO: 5 shows the amino acid sequence of KEY44978.11: 16-277 ofcurli production assembly/transport protein CsgG [Citrobacteramalonaticus], which is 98% identical to SEQ ID NO: 2.

SEQ ID NO: 6 shows the amino acid sequence of YP_003364699.1: 16-277 ofcurli production assembly/transport component [Citrobacter rodentiumICC168], which is 97% identical to SEQ ID NO: 2.

SEQ ID NO: 7 shows the amino acid sequence of YP_004828099.1: 16-277 ofcurli production assembly/transport component CsgG [Enterobacterasburiae LF7a], which is 94% identical to SEQ ID NO: 2.

SEQ ID NO: 8 shows the polynucleotide sequence encoding the Phi29 DNApolymerase.

SEQ ID NO: 9 shows the amino acid sequence of the Phi29 DNA polymerase.

SEQ ID NO: 10 shows the codon optimised polynucleotide sequence derivedfrom the sbcB gene from E. coli. It encodes the exonuclease I enzyme(EcoExo I) from E. coli.

SEQ ID NO: 11 shows the amino acid sequence of exonuclease I enzyme(EcoExo I) from E. coli.

SEQ ID NO: 12 shows the codon optimised polynucleotide sequence derivedfrom the xthA gene from E. coli. It encodes the exonuclease III enzymefrom E. coli.

SEQ ID NO: 13 shows the amino acid sequence of the exonuclease IIIenzyme from E. coli. This enzyme performs distributive digestion of 5′monophosphate nucleosides from one strand of double stranded DNA (dsDNA)in a 3′-5′ direction. Enzyme initiation on a strand requires a 5′overhang of approximately 4 nucleotides.

SEQ ID NO: 14 shows the codon optimised polynucleotide sequence derivedfrom the recJ gene from T. thermophilus. It encodes the RecJ enzyme fromT. thermophilus (TthRecJ-cd).

SEQ ID NO: 15 shows the amino acid sequence of the RecJ enzyme from T.thermophilus (TthRecJ-cd). This enzyme performs processive digestion of5′ monophosphate nucleosides from ssDNA in a 5′ 3′ direction. Enzymeinitiation on a strand requires at least 4 nucleotides.

SEQ ID NO: 16 shows the codon optimised polynucleotide sequence derivedfrom the bacteriophage lambda exo (redX) gene. It encodes thebacteriophage lambda exonuclease.

SEQ ID NO: 17 shows the amino acid sequence of the bacteriophage lambdaexonuclease. The sequence is one of three identical subunits thatassemble into a trimer. The enzyme performs highly processive digestionof nucleotides from one strand of dsDNA, in a 5′-3′direction(http://www.neb.com/nebecomm/products/productM0262.asp). Enzymeinitiation on a strand preferentially requires a 5′ overhang ofapproximately 4 nucleotides with a 5′ phosphate.

SEQ ID NO: 18 shows the amino acid sequence of He1308 Mbu.

SEQ ID NO: 19 shows the amino acid sequence of He1308 Csy.

SEQ ID NO: 20 shows the amino acid sequence of He1308 Tga.

SEQ ID NO: 21 shows the amino acid sequence of He1308 Mhu.

SEQ ID NO: 22 shows the amino acid sequence of TraI Eco.

SEQ ID NO: 23 shows the amino acid sequence of XPD Mbu.

SEQ ID NO: 24 shows the amino acid sequence of Dda 1993.

SEQ ID NO: 25 shows the amino acid sequence of Trwc Cba.

SEQ ID NO: 26 shows the amino acid sequence of WP_006819418.1: 19-280 oftransporter [Yokenella regensburgei], which is 91% identical to SEQ IDNO: 2.

SEQ ID NO: 27 shows the amino acid sequence of WP_024556654.1: 16-277 ofcurli production assembly/transport protein CsgG [Cronobacter pulveris],which is 89% identical to SEQ ID NO: 2.

SEQ ID NO: 28 shows the amino acid sequence of YP_005400916.1:16-277 ofcurli production assembly/transport protein CsgG [Rahnella aquatilisHX2], which is 84% identical to SEQ ID NO: 2.

SEQ ID NO: 29 shows the amino acid sequence of KFC99297.1: 20-278 ofCsgG family curli production assembly/transport component [Kluyveraascorbata ATCC 33433], which is 82% identical to SEQ ID NO: 2.

SEQ ID NO: 30 shows the amino acid sequence of KFC86716.11:16-274 ofCsgG family curli production assembly/transport component [Hafnia alveiATCC 13337], which is 81% identical to SEQ ID NO: 2.

SEQ ID NO: 31 shows the amino acid sequence of YP_007340845.11:16-270 ofuncharacterised protein involved in formation of curli polymers[Enterobacteriaceae bacterium strain FGI 57], which is 76% identical toSEQ ID NO: 2.

SEQ ID NO: 32 shows the amino acid sequence of WP_010861740.1: 17-274 ofcurli production assembly/transport protein CsgG [Plesiomonasshigelloides], which is 70% identical to SEQ ID NO: 2.

SEQ ID NO: 33 shows the amino acid sequence of YP 205788.1: 23-270 ofcurli production assembly/transport outer membrane lipoprotein componentCsgG [Vibrio fischeri ES114], which is 60% identical to SEQ ID NO: 2.

SEQ ID NO: 34 shows the amino acid sequence of WP_017023479.1: 23-270 ofcurli production assembly protein CsgG [Aliivibrio logei], which is 59%identical to SEQ ID NO: 2.

SEQ ID NO: 35 shows the amino acid sequence of WP_007470398.1: 22-275 ofCurli production assembly/transport component CsgG [Photobacterium sp.AK15], which is 57% identical to SEQ ID NO: 2.

SEQ ID NO: 36 shows the amino acid sequence of WP_021231638.1: 17-277 ofcurli production assembly protein CsgG [Aeromonas veronii], which is 56%identical to SEQ ID NO: 2.

SEQ ID NO: 37 shows the amino acid sequence of WP_033538267.1: 27-265 ofcurli production assembly/transport protein CsgG [Shewanella sp.ECSMB14101], which is 56% identical to SEQ ID NO: 2.

SEQ ID NO: 38 shows the amino acid sequence of WP_003247972.1: 30-262 ofcurli production assembly protein CsgG [Pseudomonas putida], which is54% identical to SEQ ID NO: 2.

SEQ ID NO: 39 shows the amino acid sequence of YP_003557438.1: 1-234 ofcurli production assembly/transport component CsgG [Shewanella violaceaDS S12], which is 53% identical to SEQ ID NO: 2.

SEQ ID NO: 40 shows the amino acid sequence of WP_027859066.1: 36-280 ofcurli production assembly/transport protein CsgG [Marinobacteriumjannaschii], which is 53% identical to SEQ ID NO: 2.

SEQ ID NO: 41 shows the amino acid sequence of CEJ70222.1: 29-262 ofCurli production assembly/transport component CsgG [Chryseobacteriumoranimense G311], which is 50% identical to SEQ ID NO: 2.

SEQ ID NO: 42 shows a polynucleotide sequence used in Example 2.

SEQ ID NO: 43 shows a polynucleotide sequence used in Example 2.

SEQ ID NO: 44 shows a polynucleotide sequence used in Example 2.

SEQ ID NO: 45 shows a polynucleotide sequence used in Example 2.

SEQ ID NO: 46 shows a polynucleotide sequence used in Example 2.Attached to the 3′ end of SEQ ID NO: 46 is six iSp18 spacers which areattached at the opposite end to two thymines and a 3′ cholesterol TEG.

SEQ ID NO: 47 shows the polynucleotide sequence of StrepII(C).

SEQ ID NO: 48 shows the polynucleotide sequence of Pro.

SEQ ID NO: 49 shows the codon optimised polynucleotide sequence encodingthe wild-type MspA monomer. This mutant lacks the signal sequence.

SEQ ID NO: 50 shows the amino acid sequence of the mature form of thewild-type MspA monomer. This mutant lacks the signal sequence.

SEQ ID NO: 51 shows the polynucleotide sequence of Thrombin BindingAptamer used in Examples 7 and 11.

SEQ ID NO: 52 shows the polynucleotide sequence of a Y-adaptor topstrand.

SEQ ID NO: 53 shows the polynucleotide sequence of a Y-adaptor blockerstrand.

SEQ ID NO: 54 shows the polynucleotide sequence of a Y-adaptorcholesterol tether strand.

SEQ ID NO: 55 shows the polynucleotide sequence of a Y-adaptor bottomstrand.

SEQ ID NO: 56 shows the polynucleotide sequence of a 3.6 kb doublestranded DNA target sequence used in the Examples.

DETAILED DESCRIPTION OF THE INVENTION

It is to be understood that different applications of the disclosedproducts and methods may be tailored to the specific needs in the art.It is also to be understood that the terminology used herein is for thepurpose of describing particular embodiments of the invention only, andis not intended to be limiting.

In addition as used in this specification and the appended claims, thesingular forms “a”, “an”, and “the” include plural referents unless thecontent clearly dictates otherwise. Thus, for example, reference to “apolynucleotide” includes two or more polynucleotides, reference to “apolynucleotide binding protein” includes two or more such proteins,reference to “a helicase” includes two or more helicases, reference to“a monomer” refers to two or more monomers, reference to “a pore”includes two or more pores and the like.

All publications, patents and patent applications cited herein, whethersupra or infra, are hereby incorporated by reference in their entirety.

Mutant CsgG Monomers

An aspect of the invention provides mutant CsgG monomers. The mutantCsgG monomers may be used to form the pores of the invention. A mutantCsgG monomer is a monomer whose sequence varies from that of a wild-typeCsgG monomer and which retains the ability to form a pore. Methods forconfirming the ability of mutant monomers to form pores are well-knownin the art and are discussed in more detail below.

Pores constructed from the CsGG monomers of some embodiments of theinvention comprising the modification R97W display an increased accuracyas compared to otherwise identical pores without the modification at 97when characterizing (or sequencing) target polynucleotides. An increasedaccuracy is also seen when instead of R97W the CsgG monomers of theinvention comprise the modification R93W or the modifications R93Y andR97Y. Accordingly, pores may be constructed from one or more mutant CsgGmonomers that comprise a modification at R97 or R93 of SEQ ID NO: 2 suchthat the modification increases the hydrophobicity of the amino acid.For example, such modification may include an amino acid substitutionwith any amino acid containing a hydrophobic side chain, including,e.g., but not limited to W and Y.

The CsgG monomers of the invention that comprise R192D/Q/F/S/T areeasier to express than monomers which do not have a substitution atposition 192 which may be due to the reduction of positive charge.Accordingly position 192 may be substituted with an amino-acid whichreduces the positive charge. The monomers of the invention that compriseR192D/Q/F/S/T may also comprise additional modifications which improvethe ability of mutant pores formed from the monomers to interact withand characterise analytes, such as polynucleotides.

The CsgG monomers of some embodiments of the invention that comprise adeletion of V105, A106 and I107, a deletion of F193, I194, D195, Y196,Q197, R198 and L199 or a deletion of D195, Y196, Q197, R198 and L199,and/or F191T display an increased accuracy when characterizing (orsequencing) target polynucleotides.

Pores comprising the CsgG monomers of some embodiments of the inventionthat comprise K94Q or K94N show a reduction in the number of noisy pores(namely those pores that give rise to an increased signal:noise ratio)as compared to identical pores without the mutation at 94 whencharacterizing (or sequencing) target polynucleotides. Position 94 isfound within the vestibule of the pore and was found to be aparticularly sensitive position in relation to the noise of the currentsignal. Pores comprising the CsgG monomers of some embodiments of theinvention that comprise T104K or T104R, N91R, E101K/N/Q/T/H, E44N/Q,Q114K, A99R, I95R, N91R, L90R, E44Q/N and/or Q42K all demonstrate animproved ability to capture target polynucleotides when used tocharacterize (or sequence) target polynucleotides as compared toidentical pores without substitutions at these positions.

Characterisation, such as sequencing, of a polynucleotide using atransmembrane pore may be carried out such as disclosed in InternationalApplication No. PCT/GB2012/052343 (published as WO 2013/041878). As thetarget polynucleotide moves with respect to, or through the pore, theanalyte may be characterised from the distinctive ion current signatureproduced, typically by measuring the ion current flow through the pore.The level of current measured at any particular time is typicallydependent on a group of k polymer (for example nucleotide) units where kis a positive integer and the typical current signature may berepresented as a series of current levels indicative of a particulark-mer. The movement of the polynucleotide with respect to, such asthrough, the pore can be viewed as movement from one k-mer to another orfrom k-mer to k-mer. Analytical techniques to characterise thepolynucleotide may for example involve the use of an HMM, a neuralnetwork and for example a Forwards Backwards algorithm or Viterbialgorithm to determine the likelihood of the series of measurementscorresponding to a particular sequence. Alternatively the polynucleotidemay be characterised by determining a feature vector and comparing thefeature vector to another feature vector, which may be known, such asdisclosed in International Application No. PCT/GB2013/050381 (publishedas WO 2013/121224). However, the analytical techniques used tocharacterise the polynucleotide are not necessarily restricted to theabove examples.

When a monomer of the invention forms a transmembrane pore and is usedwith a polynucleotide binding protein to characterise a targetpolynucleotide, some of the modified positions interact with thepolynucleotide binding protein. For example, when the monomer forms atransmembrane pore and is used with a polynucleotide binding protein tocharacterise a target polynucleotide, R97W interacts with thepolynucleotide binding protein. Modifying the CsgG monomer in accordancewith the invention typically provides more consistent movement of thetarget polynucleotide with respect to, such as through, a transmembranepore comprising the monomer. The modification(s) typically provide moreconsistent movement from one k-mer to another or from k-mer to k-mer asthe target polynucleotide moves with respect to, such as through, thepore. The modification(s) typically allow the target polynucleotide tomove with respect to, such as through, the transmembrane pore moresmoothly. The modification(s) typically provide more regular or lessirregular movement of the target polynucleotide with respect to, such asthrough, the transmembrane pore.

Modifying the CsgG monomer in accordance with the invention (e.g. R97W)typically reduces the amount of slipping forward associated with themovement of the target polynucleotide with respect to, such as through,a pore comprising the monomer. Some helicases including the Dda helicaseused in the Example move along the polynucleotide in a 5′ to 3′direction. When the 5′end of the polynucleotide (the end away from whichthe helicase moves) is captured by the pore, the helicase works with thedirection of the field resulting from the applied potential and movesthe threaded polynucleotide into the pore and into the trans chamber.Slipping forward involves the DNA moving forwards relative to the thepore (i.e. towards its 3′ and away from its 5′ end) at least 4consecutive nucleotides and typically more than 10 consecutivenucleotides. Slipping forward may involve movement forward of 100consecutive nucleotides or more and this may happen more than once ineach strand.

Modifying the CsgG monomer in accordance with the invention (e.g. R97W)typically reduces the noise associated with the movement of the targetpolynucleotide with respect to, such as through, a transmembrane porecomprising the monomer. Unwanted movement of the target polynucleotidein any dimension as the signal is being analysed typically results innoise in the current signature or level for the k-mer. The modificationmay reduce this noise by reducing unwanted movement associated with oneor more k-mers, such as each k-mer, in the target polynucleotide. Themodification may reduce the noise associated with the current level orsignature for one or more k-mers, such as each k-mer, in the targetpolynucleotide.

The enzyme motors employed for moving the polynucleotide have multiplesub-steps in the full catalytic cycle where ATP is hydrolysed to movethe polynucleotide forward one base (eg. binding ATP.Mg, hydrolysing toproduce ADP.P.Mg, moving the polynucleotide one base forward, andreleasing the ADP/P/Mg by-products). Each sub-step process has acharacteristic dwell time distribution determined by the kinetics of theprocess. If any of these sub-steps of the catalytic cycle move theposition of the polynucleotide in the reader (e.g. by moving thepolynucleotide relative to the enzyme, or by changing the position ofthe enzyme on the top of the pore) then this may be observed as a changein current through the pore, as long the change lasts sufficiently longto be detected by the acquisition electronics. If the sub-step processesresult in no change of conformation or shift in polynucleotide, or occurtoo quickly to observe, then in an ideal system the full catalytic cyclewill result in only one step change in current for the polynucleotidemoving one integer base forward.

For pores that do not contain R97W (egPro-CP1-Eco-(WT-Y51A/F56Q-StrepII(C))9), we observe long dwell timelevels where predicted by the model, with an approximately exponentialdwell distribution that is dependent on ATP.Mg concentration. For poreAQwe also short-lived substeps current levels in between the major levels,as marked in FIG. 48. Because the sub-step current levels areshort-lived, they are most easily observed in the gap between two widelyseparated current levels. The sub-steps levels correspond to anintermediate approximately 0.5 base movement of the polynucleteotide,and under these conditions have an ATP.Mg independent dwell time ofapproximately 3 milliseconds.

Pores containing R97W (e.g. Pro-CP1-Eco-(WT-Y51A/F56Q/R97W-StrepII(C))9)shows similar longer lived main levels with ATP.Mg dependent dwelltimes, but shows no signs of distinct intermediate sub-step currentlevels under these conditions or at this acquisition frequency (possibleexplanations being that they do not occur, occur too quickly to beobserved, or that the substeps do occur and are slow enough in principleto be observed but that in practice they are not observed due to forexample the way in which the enzyme interacts with the pore).

The raw data traces (FIG. 48) show the ionic current (y-axis, pA) vs.time (x-axis, seconds) trace of an enzyme controlled DNA strandtranslocation through a nanopore for the poresPro-CP1-Eco-(WT-Y51A/F56Q/R97W-StrepII(C))9 (Pore 97W) andPro-CP1-Eco-(WT-Y51A/F56Q-StrepII(C))9 (Pore AQ). Each current level isthe result of the sequence held in the nanopore reader altering the flowof ions, and step-wise changes in current are observed when thepolynucleotide changes position in the nanopore, for example when theenzyme moves the entire strand forward one base. In this case the DNAstrand contains in part a repeating sequence (GGTT)n. The data wasacquired by loading a Dda enzyme onto synthetic DNA polynucleotides andrunning on a MinION recording raw data output (Cis buffer: 500 mM KCl,25 mM HEPES, pH8, 0.6 mM MgCl2, 0.6 mM ATP, 140 mV, 37 degC, 5 kHzacquisition frequency). Pore97W only shows the main current levels frominteger step-wise movements of the polynucleotide, with no significantdata density between the levels. In comparison, PoreAQ has significantintermediate sub-step levels, as marked by the arrows in FIG. 48.

The mutant monomers preferably have improved polynucleotide readingproperties i.e. display improved polynucleotide capture and nucleotidediscrimination. In particular, pores constructed from the mutantmonomers preferably capture nucleotides and polynucleotides more easilythan the wild type. In addition, pores constructed from the mutantmonomers preferably display an increased current range, which makes iteasier to discriminate between different nucleotides, and a reducedvariance of states, which increases the signal-to-noise ratio.

In addition, the number of nucleotides contributing to the current asthe polynucleotide moves through pores constructed from the mutants ispreferably decreased. This makes it easier to identify a directrelationship between the observed current as the polynucleotide movesthrough the pore and the polynucleotide sequence. In addition, poresconstructed from the mutant monomers may display an increasedthroughput, i.e. are more likely to interact with an analyte, such as apolynucleotide. This makes it easier to characterise analytes using thepores. Pores constructed from the mutant monomers may insert into amembrane more easily. A mutant monomer of the invention comprises avariant of the sequence shown in SEQ ID NO: 2. SEQ ID NO: 2 is thewild-type CsgG monomer from Escherichia coli Str. K-12 substr. MC4100. Avariant of SEQ ID NO: 2 is a polypeptide that has an amino acid sequencewhich varies from that of SEQ ID NO: 2 and which retains its ability toform a pore. The ability of a variant to form a pore can be assayedusing any method known in the art. For instance, the variant may beinserted into an amphiphilic layer along with other appropriate subunitsand its ability to oligomerise to form a pore may be determined. Methodsare known in the art for inserting subunits into membranes, such asamphiphilic layers. For example, subunits may be suspended in a purifiedform in a solution containing a triblock copolymer membrane such that itdiffuses to the membrane and is inserted by binding to the membrane andassembling into a functional state.

In all of the discussion herein, the standard one letter codes for aminoacids are used. These are as follows: alanine (A), arginine (R),asparagine (N), aspartic acid (D), cysteine (C), glutamic acid (E),glutamine (Q), glycine (G), histidine (H), isoleucine (I), leucine (L),lysine (K), methionine (M), phenylalanine (F), proline (P), serine (S),threonine (T), tryptophan (W), tyrosine (Y) and valine (V). Standardsubstitution notation is also used, i.e. Q42R means that Q at position42 is replaced with R.

In one embodiment of the mutant monomers of the invention, the variantof SEQ ID NO: 2 comprises (a) one or more mutations at the followingpositions (i.e. mutations at one or more of the following positions)I41, R93, A98, Q100, G103, T104, A106, I107, N108, L113, S115, T117,Y130, K135, E170, S208, D233, D238 and E244 and/or (b) one or more ofD43S, E44S, F48S/N/Q/Y/W/I/V/H/R/K, Q87N/R/K, N91K/R, K94R/F/Y/W/L/S/N,R97F/Y/W/V/I/K/S/Q/H, E101I/L/A/H, N102K/Q/L/I/V/S/H, R110F/G/N,Q114R/K, R142Q/S, T150Y/A/V/L/S/Q/N, R192D/Q/F/S/T and D248S/N/Q/K/R.The variant may comprise (a); (b); or (a) and (b).

In some embodiments of the invention, the variant of SEQ ID NO: 2comprises R97W. In some embodiments of the invention, the variant of SEQID NO: 2 comprises R192D/Q/F/S/T, preferably R192D/Q. more preferablyR192D. In (a), the variant may comprise modifications at any number andcombination of the positions, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18 or 19 of the positions. In (a), the variantpreferably comprises one or more of I41N, R93F/Y/W/L/I/V/N/Q/S, A98K/R,Q100K/R, G103F/W/S/N/K/R, T104R/K, A106R/K, I107R/K/W/F/Y/L/V, N108R/K,L113K/R, S115R/K, T117R/K, Y130W/F/H/Q/N, K135L/V/N/Q/S, E 170S/N/Q/K/R,S208V/I/F/W/Y/L/T, D233S/N/Q/K/R, D238S/N/Q/K/R and E244S/N/Q/K/R.

In (a), the variant preferably comprises one or more modifications whichprovide more consistent movement of a target polynucleotide with respectto, such as through, a transmembrane pore comprising the monomer. Inparticular, in (a), the variant preferably comprises one or moremutations at the following positions (i.e. mutations at one or more ofthe following positions) R93, G103 and I107. The variant may compriseR93; G103; I107; R93 and G103; R93 and I107; G103 and I107; or R93, G103and I107. The variant preferably comprises one or more ofR93F/Y/W/L/I/V/N/Q/S, G103F/W/S/N/K/R and I107R/K/W/F/Y/L/V. These maybe present in any combination shown for the positions R93, G103 andI107.

In (a), the variant preferably comprises one or modifications whichallow pores constructed from the mutant monomers preferably capturenucleotides and polynucleotides more easily. In particular, in (a), thevariant preferably comprises one or more mutations at the followingpositions (i.e. mutations at one or more of the following positions)I41, T104, A106, N108, L113, S115, T117, E170, D233, D238 and E244. Thevariant may comprise modifications at any number and combination of thepositions, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 of the positions.The variant preferably comprises one or more of I41N, T104R/K, A106R/K,N108R/K, L113K/R, S115R/K, T117R/K, E170S/N/Q/K/R, D233S/N/Q/K/R,D238S/N/Q/K/R and E244S/N/Q/K/R. Additionally or alternatively thevariant may comprise (c) Q42K/R, E44N/Q, L90R/K, N91R/K, I95R/K, A99R/K,E101H/K/N/Q/T and/or Q114K/R.

In (a), the variant preferably comprises one or more modifications whichprovide more consistent movement and increase capture. In particular, in(a), the variant preferably comprises one or more mutations at thefollowing positions (i.e. mutations at one or more of the followingpositions) (i) A98, (ii) Q100, (iii) G103 and (iv) I107. The variantpreferably comprises one or more of (i) A98R/K, (ii) Q100K/R, (iii)G103K/R and (iv) I107R/K. The variant may comprise {i}; {ii}; {iii};{iv}; {i,ii}; {i,iii}; {i,iv}; {ii,iii}; {ii,iv}; {iii,iv}; {i,ii,iii};{i,ii,iv}; {i,iii,iv}; {ii,iii,iv}; or {i,ii,iii,iv}.

Particularly preferred mutant monomers which provide for increasedcapture of analytes, such as a polynucleotides include a mutation at oneor more of positions Q42, E44, E44, L90, N91, 195, A99, E101 and Q114,which mutation removes the negative charge and/or increases the positivecharge at the mutated positions. In particular, the following mutationsmay be included in a mutant monomer of the invention to produce a CsgGpore that has an improved ability to capture an analyte, preferably apolynucleotide: Q42K, E44N, E44Q, L90R, N91R, I95R, A99R, E101H, E101K,E101N, E101Q, E101T and Q114K. Examples of particular mutant monomerswhich comprise one of these mutations in combination with otherbeneficial mutations are described in Example 11.

In (a), the variant preferably comprises one or more modifications whichprovide increased characterisation accuracy. In particular, in (a), thevariant preferably comprises one or more mutations at the followingpositions (i.e. mutations at one or more of the following positions)Y130, K135 and S208, such as Y130; K135; S208; Y130 and K135; Y130 andS208; K135 and S208; or Y130, K135 and S208. The variant preferablycomprises one or more of Y130W/F/H/Q/N, K135L/V/N/Q/S and R142Q/S. Thesesubstitutions may be present in any number and combination as set outfor Y130, K135 and S208.

In (b), the variant may comprise any number and combination of thesubstitutions, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 of thesubstitutions. In (b), the variant preferably comprises one or moremodifications which provide more consistent movement of a targetpolynucleotide with respect to, such as through, a transmembrane porecomprising the monomer. In particular, in (b), the variant preferablycomprises one or more one or more of (i) Q87N/R/K, (ii)K94R/F/Y/W/L/S/N, (iii) R97F/Y/W/V/I/K/S/Q/H, (iv) N102K/Q/L/I/V/S/H and(v) R110F/G/N. More preferably, the variant comprises K94D or K94Qand/or R97W or R97Y. The variant may comprise {i}; {ii}; {iii}; {iv};{v}; {i,ii}; {i,iii}; {i,iv}; {i,v}; {ii,iii}; {ii,iv}; {ii,v};{iii,iv}; {iii,v}; {iv,v}; {i,ii,iii}; {i,ii,iv}; {i,ii,v}; {i,iii,iv};{i,iii,v}; {i,iv,v}; {ii,iii,iv}; {ii,iii,v}; {ii,iv,v}; {iii,iv,v};{i,ii,iii,iv}; {l,ii,iii,v}; {i,ii,iv,v}; {i,iii,iv,v}; {ii,iii,iv,v};or {i,ii,iii,iv,v}. Other preferred variants that are modified toprovide more consistent movement of a target polynucleotide with respectto, such as through, a transmembrane pore comprising the monomer include(vi) R93W and R93Y. A preferred variant may comprise R93W and R97W, R93Yand R97W, R93W and R97W, or more preferably R93Y and R97Y. The variantmay comprise {vi}; {i,vi}; {ii,vi}; {iii,vi}; {iv,vi}; {v,vi};{i,ii,vi}; {i,iii,vi}; {i,iv,vi}; {i,v,vi}; {ii,iii,vi}; {ii,iv,vi};{ii,v,vi}; {iii,iv,vi}; {iii,v,vi}; {iv,v,vi}, {l,ii,iii,vi};{i,ii,iv,vi}; {i, ii,v,vi}, {i,iii,iv,vi}; {l,iii,v,vi}; {i,iv,v,vi};{ii,iii,iv,vi}; {ii,iii,v,vi}; Ili, iv,v,viL{iii, iv,v,vi},{i,ii,iii,iv,vi}, {l,ii,iii,v,vi}; {i,ii,iv,v,vi}; {i,iii,iv,v,vi};{ii,iii,iv,v,vi}; or {i,ii,iii,iv,v,vi}.

In (b), the variant preferably comprises one or modifications whichallow pores constructed from the mutant monomers preferably capturenucleotides and polynucleotides more easily. In particular, in (b), thevariant preferably comprises one or more of (i) D43S, (ii) E44S, (iii)N91K/R, (iv) Q114R/K and (v) D248S/N/Q/K/R. The variant may comprise{i}; {ii}; {iii}; {iv}; {v}; {i,ii}; {i,iii}; {i,iv}; {i,v}; {ii,iii};{ii,iv}; {ii,v}; {iii,iv}; {iii,v}; {iv,v}; {i,ii,iii}; {i,ii,iv};{i,ii,v}; {i,iii,iv}; {i,iii,v}; {i,iv,v}; {ii,iii,iv}; {ii,iii,v};{ii,iv,v}; {iii,iv,v}; {i,ii,iii,iv}; {i,ii,iii,v}; {i,ii,iv,v};{i,iii,iv,v}; {ii,iii,iv,v}; or {i,ii,iii,iv,v}.

In (b), the variant preferably comprises one or more modifications whichprovide more consistent movement and increase capture. In particular, in(b), the variant preferably comprises one or more of Q87R/K, E101I/L/A/Hand N102K, such as Q87R/K; E101I/L/A/H; N102K; Q87R/K and E101I/L/A/H;Q87R/K and N102K; E101I/L/A/H and N102K; or Q87R/K, E101I/L/A/H andN102K.

In (b), the variant preferably comprises one or more modifications whichprovide increased characterisation accuracy. In particular, in (a), thevariant preferably comprises F48S/N/Q/Y/W/I/V.

In (b), the variant preferably comprises one or more modifications whichprovide increased characterisation accuracy and increased capture. Inparticular, in (a), the variant preferably comprises F48H/R/K.

The variant may comprise modifications in both (a) and (b) which providemore consistent movement. The variant may comprise modifications in both(a) and (b) which provide increased capture.

The invention provides variants of SEQ ID NO: 2 which provide anincreased throughput of an assay for characterising an analyte, such asa polynucleotide, using a pore comprising the variant. Such variants maycomprise a mutation at K94, preferably K94Q or K94N, more preferablyK94Q. Examples of particular mutant monomers which comprise a K94Q orK94N mutation in combination with other beneficial mutations aredescribed in Examples 10 and 11.

The invention provides variants of SEQ ID NO: 2 which provide increasedcharacterisation accuracy in an assay for characterising an analyte,such as a polynucleotide, using a pore comprising the variant. Suchvariants include variants that comprise: a mutation at F191, preferablyF191T; deletion of V105-I107; deletion of F193-L199 or of D195-L199;and/or a mutation at R93 and/or R97, preferably R93Y, R97Y, or morepreferably, R97W, R93W or both R97Y and R97Y. Examples of particularmutant monomers which comprise one or more of these mutations incombination with other beneficial mutations are described in Example 9.

In another embodiment of the mutant monomers of the invention, thevariant of SEQ ID NO: 2 comprises (A) deletion of one or more positionsR192, F193, I194, D195, Y196, Q197, R198, L199, L200 and E201 and/or (B)deletion of one or more of V139/G140/D149/T150/V186/Q187/V204/G205(called band 1 herein), G137/G138/Q151/Y152/Y184/E185/Y206/T207 (calledband 2 herein) and A141/R142/G147/A148/A188/G189/G202/E203 (called band3 herein).

In (A), the variant may comprise deletion of any number and combinationof the positions, such as 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 of thepositions. In (A), the variant preferably comprises deletion of

-   -   D195, Y196, Q197, R198 and L199;    -   R192, F193, I194, D195, Y196, Q197, R198, L199 and L200;    -   Q197, R198, L199 and L200;    -   I194, D195, Y196, Q197, R198 and L199;    -   D195, Y196, Q197, R198, L199 and L200;    -   Y196, Q197, R198, L199, L200 and E201;    -   Q197, R198, L199, L200 and E201;    -   Q197, R198, L199; or    -   F193, I194, D195, Y196, Q197, R198 and L199.        More preferably, the variant comprises deletion of D195, Y196,        Q197, R198 and L199 or F193, I194, D195, Y196, Q197, R198 and        L199. In (B), any number and combination of bands 1 to 3 may be        deleted, such as band 1; band 2; band 3; bands 1 and 2; bands 1        and 3; bands 2 and 3; or bands 1, 2 and 3.

The variant may comprise deletions according to (A); (B); or (A) and(B).

The variants comprising deletion of one or more positions according to(A) and/or (B) above may further comprise any of the modifications orsubstitutions discussed above and below. If the modifications orsubstitutions are made at one or more positions which appear after thedeletion positions in SEQ ID NO: 2, the numbering of the one or morepositions of the modifications or substitutions must be adjustedaccordingly. For instance, if L199 is deleted, E244 becomes E243.Similarly, if band 1 is deleted, R192 becomes R186.

In another embodiment of the mutant monomers of the invention, thevariant of SEQ ID NO: 2 comprises (C) deletion of one or more positionsV105, A106 and I107. The deletions in accordance with (C) may be made inaddition to deletions according to (A) and/or (B).

The above-described deletions typically reduce the noise associated withthe movement of the target polynucleotide with respect to, such asthrough, a transmembrane pore comprising the monomer. As a result thetarget polynucleotide can be characterised more accurately.

In the paragraphs above where different amino acids at a specificposition are separated by the/symbol, the/symbol means “or”. Forinstance, Q87R/K means Q87R or Q87K.

The invention provides variants of SEQ ID NO: 2 which provide increasedcapture of an an analyte, such as a polynucleotide. Such variants maycomprise a mutation at T104, preferably T104R or T104K, a mutation atN91, preferably N91R, a mutation at E101, preferably E101K/N/Q/T/H, amutation at position E44, preferably E44N or E44Q and/or a mutation atposition Q42, preferably Q42K.

The mutations at different positions in SEQ ID NO: 2 may be combined inany possible way. In particular, a monomer of the invention may compriseone or more mutation that improves accuracy, one ore more mutation thatreduces noise and/ore one or more mutation that enhances capture of ananalyte.

In the mutant monomers of the invention, the variant of SEQ ID NO: 2preferably comprises one or more of the following (i) one or moremutations at the following positions (i.e. mutations at one or more ofthe following positions) N40, D43, E44, S54, S57, Q62, R97, E101, E124,E131, R142, T150 and R192, such as one or more mutations at thefollowing positions (i.e. mutations at one or more of the followingpositions) N40, D43, E44, S54, S57, Q62, E101, E131 and T150 or N40,D43, E44, E101 and E131; (ii) mutations at Y51/N55, Y51/F56, N55/F56 orY51/N55/F56; (iii) Q42R or Q42K; (iv) K49R; (v) N102R, N102F, N102Y orN102W; (vi) D149N, D149Q or D149R; (vii) E185N, E185Q or E185R; (viii)D195N, D195Q or D195R; (ix) E201N, E201Q or E201R; (x) E203N, E203Q orE203R; and (xi) deletion of one or more of the following positions F48,K49, P50, Y51, P52, A53, S54, N55, F56 and S57. The variant may compriseany combination of (i) to (xi). 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If the variant comprises any one of (i) and (iii) to (xi), it mayfurther comprise a mutation at one or more of Y51, N55 and F56, such asat Y51, N55, F56, Y51/N55, Y51/F56, N55/F56 or Y51/N55/F56.

In (i), the variant may comprises mutations at any number andcombination of N40, D43, E44, S54, S57, Q62, R97, E101, E124, E131,R142, T150 and R192. In (i), the variant preferably comprises one ormore mutations at at the following positions (i.e. mutations at one ormore of the following positions) N40, D43, E44, S54, S57, Q62, E101,E131 and T150. In (i), the variant preferably comprises one or moremutations at the following positions (i.e. mutations at one or more ofthe following positions) N40, D43, E44, E101 and E131. In (i), thevariant preferably comprises a mutation at S54 and/or S57. In (i), thevariant more preferably comprises a mutation at (a) S54 and/or S57 and(b) one or more of Y51, N55 and F56, such as at Y51, N55, F56, Y51/N55,Y51/F56, N55/F56 or Y51/N55/F56. If S54 and/or S57 are deleted in (xi),it/they cannot be mutated in (i) and vice versa. In (i), the variantpreferably comprises a mutation at T150, such as T150I. Alternativelythe variant preferably comprises a mutation at (a) T150 and (b) one ormore of Y51, N55 and F56, such as at Y51, N55, F56, Y51/N55, Y51/F56,N55/F56 or Y51/N55/F56. In (i), the variant preferably comprises amutation at Q62, such as Q62R or Q62K. Alternatively the variantpreferably comprises a mutation at (a) Q62 and (b) one or more of Y51,N55 and F56, such as at Y51, N55, F56, Y51/N55, Y51/F56, N55/F56 orY51/N55/F56. The variant may comprise a mutation at D43, E44, Q62 or anycombination thereof, such as D43, E44, Q62, D43/E44, D43/Q62, E44/Q62 orD43/E44/Q62. Alternatively the variant preferably comprises a mutationat (a) D43, E44, Q62, D43/E44, D43/Q62, E44/Q62 or D43/E44/Q62 and (b)one or more of Y51, N55 and F56, such as at Y51, N55, F56, Y51/N55,Y51/F56, N55/F56 or Y51/N55/F56.

In (ii) and elsewhere in this application where different positions areseparated by the / symbol, the/symbol means “and” such that Y51/N55 isY51 and N55. In (ii), the variant preferably comprises mutations atY51/N55. It has been proposed that the constriction in CsgG is composedof three stacked concentric rings formed by the side chains of residuesY51, N55 and F56 (Goyal et al, 2014, Nature, 516, 250-253). Mutation ofthese residues in (ii) may therefore decrease the number of nucleotidescontributing to the current as the polynucleotide moves through the poreand thereby make it easier to identify a direct relationship between theobserved current (as the polynucleotide moves through the pore) and thepolynucleotide. F56 may be mutated in any of the ways discussed belowwith reference to variants and pores useful in the method of theinvention.

In (v), the variant may comprise N102R, N102F, N102Y or N102W. Thevariant preferably comprises (a) N102R, N102F, N102Y or N102W and (b) amutation at one or more of Y51, N55 and F56, such as at Y51, N55, F56,Y51/N55, Y51/F56, N55/F56 or Y51/N55/F56.

In (xi), any number and combination of K49, P50, Y51, P52, A53, S54,N55, F56 and S57 may be deleted. Preferably one or more of K49, P50,Y51, P52, A53, S54, N55 and S57 may be deleted. If any of Y51, N55 andF56 are deleted in (xi), it/they cannot be mutated in (ii) and viceversa.

In (i), the variant preferably comprises one of more of the followingsubstitutions N40R, N40K, D43N, D43Q, D43R, D43K, E44N, E44Q, E44R,E44K, S54P, S57P, Q62R, Q62K, R97N, R97G, R97L, E101N, E101Q, E101R,E101K, E101F, E101Y, E101W, E124N, E124Q, E124R, E124K, E124F, E124Y,E124W, E131D, R142E, R142N, T150I, R192E and R192N, such as one or moreof N40R, N40K, D43N, D43Q, D43R, D43K, E44N, E44Q, E44R, E44K, S54P,S57P, Q62R, Q62K, E101N, E101Q, E101R, E101K, E101F, E101Y, E101W, E131Dand T150I, or one or more of N40R, N40K, D43N, D43Q, D43R, D43K, E44N,E44Q, E44R, E44K, E101N, E101Q, E101R, E101K, E101F, E101Y, E101W andE131D. The variant may comprise any number and combination of thesesubstitutions. In (i), the variant preferably comprises S54P and/orS57P. In (i), the variant preferably comprises (a) S54P and/or S57P and(b) a mutation at one or more of Y51, N55 and F56, such as at Y51, N55,F56, Y51/N55, Y51/F56, N55/F56 or Y51/N55/F56. The mutations at one ormore of Y51, N55 and F56 may be any of those discussed below. In (i),the variant preferably comprises F56A/S57P or S54P/F56A. The variantpreferably comprises T150I. Alternatively the variant preferablycomprises a mutation at (a) T150I and (b) one or more of Y51, N55 andF56, such as at Y51, N55, F56, Y51/N55, Y51/F56, N55/F56 or Y51/N55/F56.

In (i), the variant preferably comprises Q62R or Q62K. Alternatively thevariant preferably comprises (a) Q62R or Q62K and (b) a mutation at oneor more of Y51, N55 and F56, such as at Y51, N55, F56, Y51/N55, Y51/F56,N55/F56 or Y51/N55/F56. The variant may comprise D43N, E44N, Q62R orQ62K or any combination thereof, such as D43N, E44N, Q62R, Q62K,D43N/E44N, D43N/Q62R, D43N/Q62K, E44N/Q62R, E44N/Q62K, D43N/E44N/Q62R orD43N/E44N/Q62K. Alternatively the variant preferably comprises (a) D43N,E44N, Q62R, Q62K, D43N/E44N, D43N/Q62R, D43N/Q62K, E44N/Q62R, E44N/Q62K,D43N/E44N/Q62R or D43N/E44N/Q62K and (b) a mutation at one or more ofY51, N55 and F56, such as at Y51, N55, F56, Y51/N55, Y51/F56, N55/F56 orY51/N55/F56.

In (i), the variant preferably comprises D43N.

In (i), the variant preferably comprises E101R, E101S, E101F or E101N.

In (i), the variant preferably comprises E124N, E124Q, E124R, E124K,E124F, E124Y, E124W or E124D, such as E124N.

In (i), the variant preferably comprises R142E and R142N.

In (i), the variant preferably comprises R97N, R97G or R97L.

In (i), the variant preferably comprises R192E and R192N.

In (ii), the variant preferably comprises F56N/N55Q, F56N/N55R,F56N/N55K, F56N/N55S, F56N/N55G, F56N/N55A, F56N/N55T, F56Q/N55Q,F56Q/N55R, F56Q/N55K, F56Q/N55S, F56Q/N55G, F56Q/N55A, F56Q/N55T,F56R/N55Q, F56R/N55R, F56R/N55K, F56R/N55S, F56R/N55G, F56R/N55A,F56R/N55T, F56S/N55Q, F56S/N55R, F56S/N55K, F56S/N55S, F56S/N55G,F56S/N55A, F56S/N55T, F56G/N55Q, F56G/N55R, F56G/N55K, F56G/N55S,F56G/N55G, F56G/N55A, F56G/N55T, F56A/N55Q, F56A/N55R, F56A/N55K,F56A/N55S, F56A/N55G, F56A/N55A, F56A/N55T, F56K/N55Q, F56K/N55R,F56K/N55K, F56K/N55S, F56K/N55G, F56K/N55A, F56K/N55T, F56N/Y51L,F56N/Y51V, F56N/Y51A, F56N/Y51N, F56N/Y51Q, F56N/Y51S, F56N/Y51G,F56Q/Y51L, F56Q/Y51V, F56Q/Y51A, F56Q/Y51N, F56Q/Y51Q, F56Q/Y51S,F56Q/Y51G, F56R/Y51L, F56R/Y51V, F56R/Y51A, F56R/Y51N, F56R/Y51Q,F56R/Y51S, F56R/Y51G, F56S/Y51L, F56S/Y51V, F56S/Y51A, F56S/Y51N,F56S/Y51Q, F56S/Y51S, F56S/Y51G, F56G/Y51L, F56G/Y51V, F56G/Y51A,F56G/Y51N, F56G/Y51Q, F56G/Y51S, F56G/Y51G, F56A/Y51L, F56A/Y51V,F56A/Y51A, F56A/Y51N, F56A/Y51Q, F56A/Y51S, F56A/Y51G, F56K/Y51L,F56K/Y51V, F56K/Y51A, F56K/Y51N, F56K/Y51Q, F56K/Y51S, F56K/Y51G,N55Q/Y51L, N55Q/Y51V, N55Q/Y51A, N55Q/Y51N, N55Q/Y51Q, N55Q/Y51S,N55Q/Y51G, N55R/Y51L, N55R/Y51V, N55R/Y51A, N55R/Y51N, N55R/Y51Q,N55R/Y51S, N55R/Y51G, N55K/Y51L, N55K/Y51V, N55K/Y51A, N55K/Y51N,N55K/Y51Q, N55K/Y51S, N55K/Y51G, N55S/Y51L, N55S/Y51V, N55S/Y51A,N55S/Y51N, N55S/Y51Q, N55S/Y51S, N55S/Y51G, N55G/Y51L, N55G/Y51V,N55G/Y51A, N55G/Y51N, N55G/Y51Q, N55G/Y51S, N55G/Y51G, N55A/Y51L,N55A/Y51V, N55A/Y51A, N55A/Y51N, N55A/Y51Q, N55A/Y51S, N55A/Y51G,N55T/Y51L, N55T/Y51V, N55T/Y51A, N55T/Y51N, N55T/Y51Q, N55T/Y51S,N55T/Y51G, F56N/N55Q/Y51L, F56N/N55Q/Y51V, F56N/N55Q/Y51A,F56N/N55Q/Y51N, F56N/N55Q/Y51Q, F56N/N55Q/Y51S, F56N/N55Q/Y51G,F56N/N55R/Y51L, F56N/N55R/Y51V, F56N/N55R/Y51A, F56N/N55R/Y51N,F56N/N55R/Y51Q, F56N/N55R/Y51S, F56N/N55R/Y51G, F56N/N55K/Y51L,F56N/N55K/Y51V, F56N/N55K/Y51A, F56N/N55K/Y51N, F56N/N55K/Y51Q,F56N/N55K/Y51S, F56N/N55K/Y51G, F56N/N55S/Y51L, F56N/N55S/Y51V,F56N/N55S/Y51A, F56N/N55S/Y51N, F56N/N55S/Y51Q, F56N/N55S/Y51S,F56N/N55S/Y51G, F56N/N55G/Y51L, F56N/N55G/Y51V, F56N/N55G/Y51A,F56N/N55G/Y51N, F56N/N55G/Y51Q, F56N/N55G/Y51S, F56N/N55G/Y51G,F56N/N55A/Y51L, F56N/N55A/Y51V, F56N/N55A/Y51A, F56N/N55A/Y51N,F56N/N55A/Y51Q, F56N/N55A/Y51S, F56N/N55A/Y51G, F56N/N55T/Y51L,F56N/N55T/Y51V, F56N/N55T/Y51A, F56N/N55T/Y51N, F56N/N55T/Y51Q,F56N/N55T/Y51S, F56N/N55T/Y51G, F56Q/N55Q/Y51L, F56Q/N55Q/Y51V,F56Q/N55Q/Y51A, F56Q/N55Q/Y51N, F56Q/N55Q/Y51Q, F56Q/N55Q/Y51S,F56Q/N55Q/Y51G, F56Q/N55R/Y51L, F56Q/N55R/Y51V, F56Q/N55R/Y51A,F56Q/N55R/Y51N, F56Q/N55R/Y51Q, F56Q/N55R/Y51S, F56Q/N55R/Y51G,F56Q/N55K/Y51L, F56Q/N55K/Y51V, F56Q/N55K/Y51A, F56Q/N55K/Y51N,F56Q/N55K/Y51Q, F56Q/N55K/Y51S, F56Q/N55K/Y51G, F56Q/N55S/Y51L,F56Q/N55S/Y51V, F56Q/N55S/Y51A, F56Q/N55S/Y51N, F56Q/N55S/Y51Q,F56Q/N55S/Y51S, F56Q/N55S/Y51G, F56Q/N55G/Y51L, F56Q/N55G/Y51V,F56Q/N55G/Y51A, F56Q/N55G/Y51N, F56Q/N55G/Y51Q, F56Q/N55G/Y51S,F56Q/N55G/Y51G, F56Q/N55A/Y51L, F56Q/N55A/Y51V, F56Q/N55A/Y51A,F56Q/N55A/Y51N, F56Q/N55A/Y51Q, F56Q/N55A/Y51S, F56Q/N55A/Y51G,F56Q/N55T/Y51L, F56Q/N55T/Y51V, F56Q/N55T/Y51A, F56Q/N55T/Y51N,F56Q/N55T/Y51Q, F56Q/N55T/Y51S, F56Q/N55T/Y51G, F56R/N55Q/Y51L,F56R/N55Q/Y51V, F56R/N55Q/Y51A, F56R/N55Q/Y51N, F56R/N55Q/Y51Q,F56R/N55Q/Y51S, F56R/N55Q/Y51G, F56R/N55R/Y51L, F56R/N55R/Y51V,F56R/N55R/Y51A, F56R/N55R/Y51N, F56R/N55R/Y51Q, F56R/N55R/Y51S,F56R/N55R/Y51G, F56R/N55K/Y51L, F56R/N55K/Y51V, F56R/N55K/Y51A,F56R/N55K/Y51N, F56R/N55K/Y51Q, F56R/N55K/Y51S, F56R/N55K/Y51G,F56R/N55S/Y51L, F56R/N55S/Y51V, F56R/N55S/Y51A, F56R/N55S/Y51N,F56R/N55S/Y51Q, F56R/N55S/Y51S, F56R/N55S/Y51G, F56R/N55G/Y51L,F56R/N55G/Y51V, F56R/N55G/Y51A, F56R/N55G/Y51N, F56R/N55G/Y51Q,F56R/N55G/Y51S, F56R/N55G/Y51G, F56R/N55A/Y51L, F56R/N55A/Y51V,F56R/N55A/Y51A, F56R/N55A/Y51N, F56R/N55A/Y51Q, F56R/N55A/Y51S,F56R/N55A/Y51G, F56R/N55T/Y51L, F56R/N55T/Y51V, F56R/N55T/Y51A,F56R/N55T/Y51N, F56R/N55T/Y51Q, F56R/N55T/Y51S, F56R/N55T/Y51G,F56S/N55Q/Y51L, F56S/N55Q/Y51V, F56S/N55Q/Y51A, F56S/N55Q/Y51N,F56S/N55Q/Y51Q, F56S/N55Q/Y51S, F56S/N55Q/Y51G, F56S/N55R/Y51L,F56S/N55R/Y51V, F56S/N55R/Y51A, F56S/N55R/Y51N, F56S/N55R/Y51Q,F56S/N55R/Y51S, F56S/N55R/Y51G, F56S/N55K/Y51L, F56S/N55K/Y51V,F56S/N55K/Y51A, F56S/N55K/Y51N, F56S/N55K/Y51Q, F56S/N55K/Y51S,F56S/N55K/Y51G, F56S/N55S/Y51L, F56S/N55S/Y51V, F56S/N55S/Y51A,F56S/N55S/Y51N, F56S/N55S/Y51Q, F56S/N55S/Y51S, F56S/N55S/Y51G,F56S/N55G/Y51L, F56S/N55G/Y51V, F56S/N55G/Y51A, F56S/N55G/Y51N,F56S/N55G/Y51Q, F56S/N55G/Y51S, F56S/N55G/Y51G, F56S/N55A/Y51L,F56S/N55A/Y51V, F56S/N55A/Y51A, F56S/N55A/Y51N, F56S/N55A/Y51Q,F56S/N55A/Y51S, F56S/N55A/Y51G, F56S/N55T/Y51L, F56S/N55T/Y51V,F56S/N55T/Y51A, F56S/N55T/Y51N, F56S/N55T/Y51Q, F56S/N55T/Y51S,F56S/N55T/Y51G, F56G/N55Q/Y51L, F56G/N55Q/Y51V, F56G/N55Q/Y51A,F56G/N55Q/Y51N, F56G/N55Q/Y51Q, F56G/N55Q/Y51S, F56G/N55Q/Y51G,F56G/N55R/Y51L, F56G/N55R/Y51V, F56G/N55R/Y51A, F56G/N55R/Y51N,F56G/N55R/Y51Q, F56G/N55R/Y51S, F56G/N55R/Y51G, F56G/N55K/Y51L,F56G/N55K/Y51V, F56G/N55K/Y51A, F56G/N55K/Y51N, F56G/N55K/Y51Q,F56G/N55K/Y51S, F56G/N55K/Y51G, F56G/N55S/Y51L, F56G/N55S/Y51V,F56G/N55S/Y51A, F56G/N55S/Y51N, F56G/N55S/Y51Q, F56G/N55S/Y51S,F56G/N55S/Y51G, F56G/N55G/Y51L, F56G/N55G/Y51V, F56G/N55G/Y51A,F56G/N55G/Y51N, F56G/N55G/Y51Q, F56G/N55G/Y51S, F56G/N55G/Y51G,F56G/N55A/Y51L, F56G/N55A/Y51V, F56G/N55A/Y51A, F56G/N55A/Y51N,F56G/N55A/Y51Q, F56G/N55A/Y51S, F56G/N55A/Y51G, F56G/N55T/Y51L,F56G/N55T/Y51V, F56G/N55T/Y51A, F56G/N55T/Y51N, F56G/N55T/Y51Q,F56G/N55T/Y51S, F56G/N55T/Y51G, F56A/N55Q/Y51L, F56A/N55Q/Y51V,F56A/N55Q/Y51A, F56A/N55Q/Y51N, F56A/N55Q/Y51Q, F56A/N55Q/Y51S,F56A/N55Q/Y51G, F56A/N55R/Y51L, F56A/N55R/Y51V, F56A/N55R/Y51A,F56A/N55R/Y51N, F56A/N55R/Y51Q, F56A/N55R/Y51S, F56A/N55R/Y51G,F56A/N55K/Y51L, F56A/N55K/Y51V, F56A/N55K/Y51A, F56A/N55K/Y51N,F56A/N55K/Y51Q, F56A/N55K/Y51S, F56A/N55K/Y51G, F56A/N55S/Y51L,F56A/N55S/Y51V, F56A/N55S/Y51A, F56A/N55S/Y51N, F56A/N55S/Y51Q,F56A/N55S/Y51S, F56A/N55S/Y51G, F56A/N55G/Y51L, F56A/N55G/Y51V,F56A/N55G/Y51A, F56A/N55G/Y51N, F56A/N55G/Y51Q, F56A/N55G/Y51S,F56A/N55G/Y51G, F56A/N55A/Y51L, F56A/N55A/Y51V, F56A/N55A/Y51A,F56A/N55A/Y51N, F56A/N55A/Y51Q, F56A/N55A/Y51S, F56A/N55A/Y51G,F56A/N55T/Y51L, F56A/N55T/Y51V, F56A/N55T/Y51A, F56A/N55T/Y51N,F56A/N55T/Y51Q, F56A/N55T/Y51S, F56A/N55T/Y51G, F56K/N55Q/Y51L,F56K/N55Q/Y51V, F56K/N55Q/Y51A, F56K/N55Q/Y51N, F56K/N55Q/Y51Q,F56K/N55Q/Y51S, F56K/N55Q/Y51G, F56K/N55R/Y51L, F56K/N55R/Y51V,F56K/N55R/Y51A, F56K/N55R/Y51N, F56K/N55R/Y51Q, F56K/N55R/Y51S,F56K/N55R/Y51G, F56K/N55K/Y51L, F56K/N55K/Y51V, F56K/N55K/Y51A,F56K/N55K/Y51N, F56K/N55K/Y51Q, F56K/N55K/Y51S, F56K/N55K/Y51G,F56K/N55S/Y51L, F56K/N55S/Y51V, F56K/N55S/Y51A, F56K/N55S/Y51N,F56K/N55S/Y51Q, F56K/N55S/Y51S, F56K/N55S/Y51G, F56K/N55G/Y51L,F56K/N55G/Y51V, F56K/N55G/Y51A, F56K/N55G/Y51N, F56K/N55G/Y51Q,F56K/N55G/Y51S, F56K/N55G/Y51G, F56K/N55A/Y51L, F56K/N55A/Y51V,F56K/N55A/Y51A, F56K/N55A/Y51N, F56K/N55A/Y51Q, F56K/N55A/Y51S,F56K/N55A/Y51G, F56K/N55T/Y51L, F56K/N55T/Y51V, F56K/N55T/Y51A,F56K/N55T/Y51N, F56K/N55T/Y51Q, F56K/N55T/Y51S, F56K/N55T/Y51G,F56E/N55R, F56E/N55K, F56D/N55R, F56D/N55K, F56R/N55E, F56R/N55D,F56K/N55E or F56K/N55D.

In (ii), the variant preferably comprises Y51R/F56Q, Y51N/F56N,Y51M/F56Q, Y51L/F56Q, Y51I/F56Q, Y51V/F56Q, Y51A/F56Q, Y51P/F56Q,Y51G/F56Q, Y51C/F56Q, Y51Q/F56Q, Y51N/F56Q, Y51S/F56Q, Y51E/F56Q,Y51D/F56Q, Y51K/F56Q or Y51H/F56Q.

In (ii), the variant preferably comprises Y51T/F56Q, Y51Q/F56Q orY51A/F56Q.

In (ii), the variant preferably comprises Y51T/F56F, Y51T/F56M,Y51T/F56L, Y51T/F56I, Y51T/F56V, Y51T/F56A, Y51T/F56P, Y51T/F56G,Y51T/F56C, Y51T/F56Q, Y51T/F56N, Y51T/F56T, Y51T/F56S, Y51T/F56E,Y51T/F56D, Y51T/F56K, Y51T/F56H or Y51T/F56R.

In (ii), the variant preferably comprises Y51T/N55Q, Y51T/N55S orY51T/N55A.

In (ii), the variant preferably comprises Y51A/F56F, Y51A/F56L,Y51A/F56I, Y51A/F56V, Y51A/F56A, Y51A/F56P, Y51A/F56G, Y51A/F56C,Y51A/F56Q, Y51A/F56N, Y51A/F56T, Y51A/F56S, Y51A/F56E, Y51A/F56D,Y51A/F56K, Y51A/F56H or Y51A/F56R.

In (ii), the variant preferably comprises Y51C/F56A, Y51E/F56A,Y51D/F56A, Y51K/F56A, Y51H/F56A, Y51Q/F56A, Y51N/F56A, Y51S/F56A,Y51P/F56A or Y51V/F56A.

In (xi), the variant preferably comprises deletion of Y51/P52,Y51/P52/A53, P50 to P52, P50 to A53, K49 to Y51, K49 to A53 andreplacement with a single proline (P), K49 to S54 and replacement with asingle P, Y51 to A53, Y51 to S54, N55/F56, N55 to S57, N55/F56 andreplacement with a single P, N55/F56 and replacement with a singleglycine (G), N55/F56 and replacement with a single alanine (A), N55/F56and replacement with a single P and Y51N, N55/F56 and replacement with asingle P and Y51Q, N55/F56 and replacement with a single P and Y51S,N55/F56 and replacement with a single G and Y51N, N55/F56 andreplacement with a single G and Y51Q, N55/F56 and replacement with asingle G and Y51S, N55/F56 and replacement with a single A and Y51N,N55/F56 and replacement with a single A/Y51Q or N55/F56 and replacementwith a single A and Y51S.

The variant more preferably comprises D195N/E203N, D195Q/E203N,D195N/E203Q, D195Q/E203Q, E201N/E203N, E201Q/E203N, E201N/E203Q,E201Q/E203Q, E185N/E203Q, E185Q/E203Q, E185N/E203N, E185Q/E203N,D195N/E201N/E203N, D195Q/E201N/E203N, D195N/E201Q/E203N,D195N/E201N/E203Q, D195Q/E201Q/E203N, D195Q/E201N/E203Q,D195N/E201Q/E203Q, D195Q/E201Q/E203Q, D149N/E201N, D149Q/E201N,D149N/E201Q, D149Q/E201Q, D149N/E201N/D195N, D149Q/E201N/D195N,D149N/E201Q/D195N, D149N/E201N/D195Q, D149Q/E201Q/D195N,D149Q/E201N/D195Q, D149N/E201Q/D195Q, D149Q/E201Q/D195Q, D149N/E203N,D149Q/E203N, D149N/E203Q, D149Q/E203Q, D149N/E185N/E201N,D149Q/E185N/E201N, D149N/E185Q/E201N, D149N/E185N/E201Q,D149Q/E185Q/E201N, D149Q/E185N/E201Q, D149N/E185Q/E201Q,D149Q/E185Q/E201Q, D149N/E185N/E203N, D149Q/E185N/E203N,D149N/E185Q/E203N, D149N/E185N/E203Q, D149Q/E185Q/E203N,D149Q/E185N/E203Q, D149N/E185Q/E203Q, D149Q/E185Q/E203Q,D149N/E185N/E201N/E203N, D149Q/E185N/E201N/E203N,D149N/E185Q/E201N/E203N, D149N/E185N/E201Q/E203N,D149N/E185N/E201N/E203Q, D149Q/E185Q/E201N/E203N,D149Q/E185N/E201Q/E203N, D149Q/E185N/E201N/E203 Q,D149N/E185Q/E201Q/E203N, D149N/E185Q/E201N/E203 Q,D149N/E185N/E201Q/E203 Q, D149Q/E185Q/E201Q/E203 Q,D149Q/E185Q/E201N/E203 Q, D149Q/E185N/E201Q/E203 Q,D149N/E185Q/E201Q/E203 Q, D149Q/E185Q/E201Q/E203N,D149N/E185N/D195N/E201N/E203N, D149Q/E185N/D195N/E201N/E203N,D149N/E185Q/D195N/E201N/E203N, D149N/E185N/D195Q/E201N/E203N,D149N/E185N/D195N/E201Q/E203N, D149N/E185N/D195N/E201N/E203 Q,D149Q/E185Q/D195N/E201N/E203N, D149Q/E185N/D195Q/E201N/E203N,D149Q/E185N/D195N/E201Q/E203N, D149Q/E185N/D195N/E201N/E203Q,D149N/E185Q/D195Q/E201N/E203N, D149N/E185Q/D195N/E201Q/E203N,D149N/E185Q/D195N/E201N/E203 Q, D149N/E185N/D195Q/E201Q/E203N,D149N/E185N/D195Q/E201N/E203 Q, D149N/E185N/D195N/E201Q/E203 Q,D149Q/E185Q/D195Q/E201N/E203N, D149Q/E185Q/D195N/E201Q/E203N,D149Q/E185Q/D195N/E201N/E203Q, D149Q/E185N/D195Q/E201Q/E203N,D149Q/E185N/D195Q/E201N/E203Q, D149Q/E185N/D195N/E201Q/E203Q,D149N/E185Q/D195Q/E201Q/E203N, D149N/E185Q/D195Q/E201N/E203 Q,D149N/E185Q/D195N/E201Q/E203 Q, D149N/E185N/D195Q/E201Q/E203 Q,D149Q/E185Q/D195Q/E201Q/E203N, D149Q/E185Q/D195Q/E201N/E203Q,D149Q/E185Q/D195N/E201Q/E203Q, D149Q/E185N/D195Q/E201Q/E203Q,D149N/E185Q/D195Q/E201Q/E203Q, D149Q/E185Q/D195Q/E201Q/E203Q,D149N/E185R/E201N/E203N, D149Q/E185R/E201N/E203N,D149N/E185R/E201Q/E203N, D149N/E185R/E201N/E203Q,D149Q/E185R/E201Q/E203N, D149Q/E185R/E201N/E203Q,D149N/E185R/E201Q/E203Q, D149Q/E185R/E201Q/E203Q,D149R/E185N/E201N/E203N, D149R/E185Q/E201N/E203N,D149R/E185N/E201Q/E203N, D149R/E185N/E201N/E203Q,D149R/E185Q/E201Q/E203N, D149R/E185Q/E201N/E203Q,D149R/E185N/E201Q/E203Q, D149R/E185Q/E201Q/E203Q,D149R/E185N/D195N/E201N/E203N, D149R/E185Q/D195N/E201N/E203N,D149R/E185N/D195Q/E201N/E203N, D149R/E185N/D195N/E201Q/E203N,D149R/E185Q/D195N/E201N/E203 Q, D149R/E185Q/D195Q/E201N/E203N,D149R/E185Q/D195N/E201Q/E203N, D149R/E185Q/D195N/E201N/E203 Q,D149R/E185N/D195Q/E201Q/E203N, D149R/E185N/D195Q/E201N/E203 Q,D149R/E185N/D195N/E201Q/E203 Q, D149R/E185Q/D195Q/E201Q/E203N,D149R/E185Q/D195Q/E201N/E203 Q, D149R/E185Q/D195N/E201Q/E203 Q,D149R/E185N/D195Q/E201Q/E203 Q, D149R/E185Q/D195Q/E201Q/E203 Q,D149N/E185R/D195N/E201N/E203N, D149Q/E185R/D195N/E201N/E203N,D149N/E185R/D195Q/E201N/E203N, D149N/E185R/D195N/E201Q/E203N,D149N/E185R/D195N/E201N/E203Q, D149Q/E185R/D195Q/E201N/E203N,D149Q/E185R/D195N/E201Q/E203N, D149Q/E185R/D195N/E201N/E203Q,D149N/E185R/D195Q/E201Q/E203N, D149N/E185R/D195Q/E201N/E203Q,D149N/E185R/D195N/E201Q/E203Q, D149Q/E185R/D195Q/E201Q/E203N,D149Q/E185R/D195Q/E201N/E203Q, D149Q/E185R/D195N/E201Q/E203Q,D149N/E185R/D195Q/E201Q/E203Q, D149Q/E185R/D195Q/E201Q/E203Q,D149N/E185R/D195N/E201R/E203N, D149Q/E185R/D195N/E201R/E203N,D149N/E185R/D195Q/E201R/E203N, D149N/E185R/D195N/E201R/E203Q,D149Q/E185R/D195Q/E201R/E203N, D149Q/E185R/D195N/E201R/E203Q,D149N/E185R/D195Q/E201R/E203Q, D149Q/E185R/D195Q/E201R/E203Q,E131D/K49R, E101N/N102F, E101N/N102Y, E101N/N102W, E101F/N102F,E101F/N102Y, E101F/N102W, E101Y/N102F, E101Y/N102Y, E101Y/N102W,E101W/N102F, E101W/N102Y, E101W/N102W, E101N/N102R, E101F/N102R,E101Y/N102R or E101W/N102F.

Preferred variants of the invention which form pores in which fewernucleotides contribute to the current as the polynucleotide movesthrough the pore comprise Y51A/F56A, Y51A/F56N, Y511/F56A, Y51L/F56A,Y51T/F56A, Y511/F56N, Y51L/F56N or Y51T/F56N or more preferablyY511/F56A, Y51L/F56A or Y51T/F56A. As discussed above, this makes iteasier to identify a direct relationship between the observed current(as the polynucleotide moves through the pore) and the polynucleotide.

Preferred variants which form pores displaying an increased rangecomprise mutations at the following positions:

Y51, F56, D149, E185, E201 and E203;

N55 and F56;

Y51 and F56;

Y51, N55 and F56; or

F56 and N102.

Preferred variants which form pores displaying an increased rangecomprise:

Y51N, F56A, D149N, E185R, E201N and E203N;

N55S and F56Q;

Y51A and F56A;

Y51A and F56N;

Y511 and F56A;

Y51L and F56A;

Y51T and F56A;

Y511 and F56N;

Y51L and F56N;

Y51T and F56N;

Y51T and F56Q;

Y51A, N55S and F56A;

Y51A, N55S and F56N;

Y51T, N55S and F56Q; or

F56Q and N102R.

Preferred variants which form pores in which fewer nucleotidescontribute to the current as the polynucleotide moves through the porecomprise mutations at the following positions:

N55 and F56, such as N55X and F56Q, wherein X is any amino acid; or

Y51 and F56, such as Y51X and F56Q, wherein X is any amino acid.

Particularly preferred variants comprise Y51A and F56Q.

Preferred variants which form pores displaying an increased throughputcomprise mutations at the following positions:

D149, E185 and E203;

D149, E185, E201 and E203; or

D149, E185, D195, E201 and E203.

Preferred variants which form pores displaying an increased throughputcomprise:

D149N, E185N and E203N;

D149N, E185N, E201N and E203N;

D149N, E185R, D195N, E201N and E203N; or

D149N, E185R, D195N, E201R and E203N.

Preferred variants which form pores in which capture of thepolynucleotide is increased comprise the following mutations:

D43N/Y51T/F56Q;

E44N/Y51T/F56Q;

D43N/E44N/Y51T/F56Q;

Y51T/F56Q/Q62R;

D43N/Y51T/F56Q/Q62R;

E44N/Y51T/F56Q/Q62R; or

D43N/E44N/Y51T/F56Q/Q62R.

Preferred variants comprise the following mutations:

D149R/E185R/E201R/E203R or Y51T/F56Q/D149R/E185R/E201R/E203R;

D149N/E185N/E201N/E203N or Y51T/F56Q/D149N/E185N/E201N/E203N;

E201R/E203R or Y51T/F56Q/E201R/E203R

E201N/E203R or Y51T/F56Q/E201N/E203R;

E203R or Y51T/F56Q/E203R;

E203N or Y51T/F56Q/E203N;

E201R or Y51T/F56Q/E201R;

E201N or Y51T/F56Q/E201N;

E185R or Y51T/F56Q/E185R;

E185N or Y51T/F56Q/E185N;

D149R or Y51T/F56Q/D149R;

D149N or Y51T/F56Q/D149N;

R142E or Y51T/F56Q/R142E;

R142N or Y51T/F56Q/R142N;

R192E or Y51T/F56Q/R192E; or

R192N or Y51T/F56Q/R192N.

Preferred variants comprise the following mutations:

Y51A/F56Q/E101N/N102R;

Y51A/F56Q/R97N/N102G;

Y51A/F56Q/R97N/N102R;

Y51A/F56Q/R97N;

Y51A/F56Q/R97G;

Y51A/F56Q/R97L;

Y51A/F56Q/N102R;

Y51A/F56Q/N102F;

Y51A/F56Q/N102G;

Y51A/F56Q/E101R;

Y51A/F56Q/E101F;

Y51A/F56Q/E101N; or

Y51A/F56Q/E101G

The variant preferably further comprises a mutation at T150. A preferredvariant which forms a pore displaying an increased insertion comprisesT150I. A mutation at T150, such as T150I, may be combined with any ofthe mutations or combinations of mutations discussed above.

A preferred variant of SEQ ID NO: 2 comprises (a) R97W and (b) amutation at Y51 and/or F56. A preferred variant of SEQ ID NO: 2comprises (a) R97W and (b) Y51R/H/K/D/E/S/T/N/Q/C/G/P/A/V/I/L/M and/orF56R/H/K/D/E/S/T/N/Q/C/G/P/A/V/I/L/M. A preferred variant of SEQ ID NO:2 comprises (a) R97W and (b) Y51L/V/A/N/Q/S/G and/or F56A/Q/N. Apreferred variant of SEQ ID NO: 2 comprises (a) R97W and (b) Y51A and/orF56Q. A preferred variant of SEQ ID NO: 2 comprises R97W, Y51A and F56Q.

In the mutant monomers of the invention, the variant of SEQ ID NO: 2preferably comprises a mutation at R192. The variant preferablycomprises R192D/Q/F/S/T/N/E, R192D/Q/F/S/T or R192D/Q. A preferredvariant of SEQ ID NO: 2 comprises (a) R97W, (b) a mutation at Y51 and/orF56 and (c) a mutation at R192, such as R192D/Q/F/S/T/N/E, R192D/Q/F/S/Tor R192D/Q. A preferred variant of SEQ ID NO: 2 comprises (a) R97W, (b)Y51R/H/K/D/E/S/T/N/Q/C/G/P/A/V/I/L/M and/orF56R/H/K/D/E/S/T/N/Q/C/G/P/A/V/I/L/M and (c) a mutation at R192, such asR192D/Q/F/S/T/N/E, R192D/Q/F/S/T or R192D/Q. A preferred variant of SEQID NO: 2 comprises (a) R97W, (b) Y51L/V/A/N/Q/S/G and/or F56A/Q/N and(c) a mutation at R192, such as R192D/Q/F/S/T/N/E, R192D/Q/F/S/T orR192D/Q. A preferred variant of SEQ ID NO: 2 comprises (a) R97W, (b)Y51A and/or F56Q and (c) a mutation at R192, such as R192 D/Q/F/S/T/N/E,R192D/Q/F/S/T or R192D/Q. A preferred variant of SEQ ID NO: 2 comprisesR97W, Y51A, F56Q and R192D/Q/F/S/T or R192D/Q. A preferred variant ofSEQ ID NO: 2 comprises R97W, Y51A, F56Q and R192D. A preferred variantof SEQ ID NO: 2 comprises R97W, Y51A, F56Q and R192Q. In the paragraphsabove where different amino acids at a specific position are separatedby the / symbol, the/symbol means “or”. For instance, R192D/Q meansR192D or R192Q.

In the mutant monomers of the invention, the variant of SEQ ID NO: 2preferably comprises a mutation at R93. A preferred variant of SEQ IDNO: 2 comprises (a) R93W and (b) a mutation at Y51 and/or F56,preferably Y51A and F56Q. D or R192N.deletion of V105, A106 and I107.

Any of the above preferred variants of SEQ ID NO: 2 may comprise aK94N/Q mutation. Any of the above preferred variants of SEQ ID NO: 2 maycomprise a F191T mutation. The invention also provides a mutant CsgGmonomer comprising a variant of the sequence shown in SEQ ID NO: 2comprising the combination of mutations present in a variant disclosedin the Examples.

Methods for introducing or substituting naturally-occurring amino acidsare well known in the art. For instance, methionine (M) may besubstituted with arginine (R) by replacing the codon for methionine(ATG) with a codon for arginine (CGT) at the relevant position in apolynucleotide encoding the mutant monomer. The polynucleotide can thenbe expressed as discussed below.

Methods for introducing or substituting non-naturally-occurring aminoacids are also well known in the art. For instance,non-naturally-occurring amino acids may be introduced by includingsynthetic aminoacyl-tRNAs in the IVTT system used to express the mutantmonomer. Alternatively, they may be introduced by expressing the mutantmonomer in E. coli that are auxotrophic for specific amino acids in thepresence of synthetic (i.e. non-naturally-occurring) analogues of thosespecific amino acids. They may also be produced by naked ligation if themutant monomer is produced using partial peptide synthesis.

Variants

In addition to the specific mutations discussed above, the variant mayinclude other mutations. Over the entire length of the amino acidsequence of SEQ ID NO: 2, a variant will preferably be at least 50%homologous to that sequence based on amino acid identity. Morepreferably, the variant may be at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90% andmore preferably at least 95%, 97% or 99% homologous based on amino acididentity to the amino acid sequence of SEQ ID NO: 2 over the entiresequence. There may be at least 80%, for example at least 85%, 90% or95%, amino acid identity over a stretch of 100 or more, for example 125,150, 175 or 200 or more, contiguous amino acids (“hard homology”).

Standard methods in the art may be used to determine homology. Forexample the UWGCG Package provides the BESTFIT program which can be usedto calculate homology, for example used on its default settings(Devereux et al (1984) Nucleic Acids Research 12, p 387-395). The PILEUPand BLAST algorithms can be used to calculate homology or line upsequences (such as identifying equivalent residues or correspondingsequences (typically on their default settings)), for example asdescribed in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S. Fet al (1990) J Mol Biol 215:403-10. Software for performing BLASTanalyses is publicly available through the National Center forBiotechnology Information (http://www.ncbi.nlm.nih.gov/).

SEQ ID NO: 2 is the wild-type CsgG monomer from Escherichia coli Str.K-12 substr. MC4100. The variant of SEQ ID NO: 2 may comprise any of thesubstitutions present in another CsgG homologue. Preferred CsgGhomologues are shown in SEQ ID NOs: 3 to 7 and 26 to 41. The variant maycomprise combinations of one or more of the substitutions present in SEQID NOs: 3 to 7 and 26 to 41 compared with SEQ ID NO: 2. For example,mutations may be made at any one or more of the positions in SEQ ID NO:2 that differ between SEQ ID NO: 2 and any one of SEQ ID NOs: 3 to 7 andSEQ ID NOs: 26 to 41. Such a mutation may be a substitution of an aminoacid in SEQ ID NO: 2 with an amino acid from the corresponding positionin any one of SEQ ID NOs: 3 to 7 and SEQ ID NOs: 26 to 41.Alternatively, the mutation at any one of these positions may be asubstitution with any amino acid, or may be a deletion or insertionmutation, such as deletion or insertion of 1 to 10 amino acids, such asof 2 to 8 or 3 to 6 amino acids. Other than the mutations disclosedherein, the amino acids that are conserved between SEQ ID NO: 2 and allof SEQ ID NOs: 3 to 7 and SEQ ID NOs: 26 to 41 are preferably present ina variant of the invention. However, conservative mutations may be madeat any one or more of these positions that are conserved between SEQ IDNO: 2 and all of SEQ ID NOs: 3 to 7 and SEQ ID NOs: 26 to 41.

The invention provides a pore-forming CsgG mutant monomer that comprisesany one or more of the amino acids described herein as being substitutedinto a specific position of SEQ ID NO: 2 at a position in the structureof the CsgG monomer that corresponds to the specific position in SEQ IDNO: 2. Corresponding positions may be determined by standard techniquesin the art. For example, the PILEUP and BLAST algorithms mentioned abovecan be used to align the sequence of a CsgG monomer with SEQ ID NO: 2and hence to identify corresponding residues.

In particular, the invention provides a pore-forming CsgG mutant monomerthat comprises any one or more of the following:

-   -   a W at a position corresponding to R97 in SEQ ID NO:2;    -   a W at a position corresponding to R93 in SEQ ID NO:2;    -   a Y at a position corresponding to R97 in SEQ ID NO: 2;    -   a Y at a position corresponding to R93 in SEQ ID NO: 2;    -   a Y at each of the positions corresponding to R93 and R97 in SEQ        ID NO: 2;    -   a D at the position corresponding to R192 in SEQ ID NO:2;    -   deletion of the residues at the positions corresponding to        V105-I107 in SEQ ID NO:2;    -   deletion of the residues at one or more of the positions        corresponding to F193 to L199 in SEQ ID NO: 2;    -   deletion of the residues the positions corresponding to F195 to        L199 in SEQ ID NO: 2;    -   deletion of the residues the positions corresponding to F193 to        L199 in SEQ ID NO: 2;    -   a T at the position corresponding to F191 in SEQ ID NO: 2;    -   a Q at the position corresponding to K49 in SEQ ID NO: 2;    -   a N at the position corresponding to K49 in SEQ ID NO: 2;    -   a Q at the position corresponding to K42 in SEQ ID NO: 2;    -   a Q at the position corresponding to E44 in SEQ ID NO: 2;    -   a N at the position corresponding to E44 in SEQ ID NO: 2;    -   a R at the position corresponding to L90 in SEQ ID NO: 2;    -   a R at the position corresponding to L91 in SEQ ID NO: 2;    -   a R at the position corresponding to I95 in SEQ ID NO: 2;    -   a R at the position corresponding to A99 in SEQ ID NO: 2;    -   a H at the position corresponding to E101 in SEQ ID NO: 2;    -   a K at the position corresponding to E101 in SEQ ID NO: 2;    -   a N at the position corresponding to E101 in SEQ ID NO: 2;    -   a Q at the position corresponding to E101 in SEQ ID NO: 2;    -   a T at the position corresponding to E101 in SEQ ID NO: 2;    -   a K at the position corresponding to Q114 in SEQ ID NO: 2.

The CsgG pore-forming monomer of the invention preferably furthercomprises an A at the position corresponding to Y51 in SEQ ID NO: 2and/or a Q at the position corresponding to F56 in SEQ ID NO: 2.

The pore-forming mutatnt monomer typically retains the ability to formthe same 3D structure as the wild-type CsgG monomer, such as the same 3Dstructure as a CsgG monomer having the sequence of SEQ ID NO: 2. The 3Dstructure of CsgG is known in the art and is disclosed, for example, inCao et al (2014) PNAS E5439-E5444. Any number of mutations may be madein the wild-type CsgG sequence in addition to the mutations describedherein provided that the CsgG mutant monomer retains the improvedproperties imparted on it by the mutations of the present invention.

Typically the CsgG monomer will retain the ability to form a structurecomprising three alpha-helicies and five beta-sheets. The presentinventors have shown in particular that mutations may be made at leastin the region of CsgG which is N-terminal to the first alpha helix(which starts at S63 in SEQ ID NO:2), in the second alpha helix (fromG85 to A99 of SEQ ID NO: 2), in the loop between the second alpha helixand the first beta sheet (from Q100 to N120 of SEQ ID NO: 2), in thefourth and fifth beta sheets (S173 to R192 and R198 to T107 of SEQ IDNO: 2, respectively) and in the loop between the fourth and fifth betasheets (F193 to Q197 of SEQ ID NO: 2) without affecting the ability ofthe CsgG monomer to form a transmembrane pore, which transmembrane poreis capable of translocating polypeptides. Therefore, it is envisagedthat further mutations may be made in any of these regions in any CsgGmonomer without affecting the ability of the monomer to form a pore thatcan translocate polynucleotides. It is also expected that mutations maybe made in other regions, such as in any of the alpha helicies (S63 toR76, G85 to A99 or V211 to L236 of SEQ ID NO: 2) or in any of the betasheets (I121 to N133, K135 to R142, I146 to R162, S173 to R192 or R198to T107 of SEQ ID NO: 2) without affecting the ability of the monomer toform a pore that can translocate polynucleotides. It is also expectedthat deletions of one or more amino acids can be made in any of the loopregions linking the alpha helicies and beta sheets and/or in theN-terminal and/or C-terminal regions of the CsgG monomer withoutaffecting the ability of the monomer to form a pore that can translocatepolynucleotides.

Amino acid substitutions may be made to the amino acid sequence of SEQID NO: 2 in addition to those discussed above, for example up to 1, 2,3, 4, 5, 10, 20 or 30 substitutions. Conservative substitutions replaceamino acids with other amino acids of similar chemical structure,similar chemical properties or similar side-chain volume. The aminoacids introduced may have similar polarity, hydrophilicity,hydrophobicity, basicity, acidity, neutrality or charge to the aminoacids they replace. Alternatively, the conservative substitution mayintroduce another amino acid that is aromatic or aliphatic in the placeof a pre-existing aromatic or aliphatic amino acid. Conservative aminoacid changes are well-known in the art and may be selected in accordancewith the properties of the 20 main amino acids as defined in Table 2below. Where amino acids have similar polarity, this can also bedetermined by reference to the hydropathy scale for amino acid sidechains in Table 3.

TABLE 2 Chemical properties of amino acids Ala aliphatic, hydrophobic,neutral Met hydrophobic, neutral Cys polar, hydrophobic, neutral Asnpolar, hydrophilic, neutral Asp polar, hydrophilic, charged (−) Prohydrophobic, neutral Glu polar, hydrophilic, charged (−) Gln polar,hydrophilic, neutral Phe aromatic, hydrophobic, neutral Arg polar,hydrophilic, charged (+) Gly aliphatic, neutral Ser polar, hydrophilic,neutral His aromatic, polar, hydrophilic, Thr polar, hydrophilic,neutral charged (+) Ile aliphatic, hydrophobic, neutral Val aliphatic,hydrophobic, neutral Lys polar, hydrophilic, charged (+) Trp aromatic,hydrophobic, neutral Leu aliphatic, hydrophobic, neutral Tyr aromatic,polar, hydrophobic

TABLE 3 Hydropathy scale Side Chain Hydropathy Ile 4.5 Val 4.2 Leu 3.8Phe 2.8 Cys 2.5 Met 1.9 Ala 1.8 Gly −0.4 Thr −0.7 Ser −0.8 Trp −0.9 Tyr−1.3 Pro −1.6 His −3.2 Glu −3.5 Gln −3.5 Asp −3.5 Asn −3.5 Lys −3.9 Arg−4.5

One or more amino acid residues of the amino acid sequence of SEQ ID NO:2 may additionally be deleted from the polypeptides described above. Upto 1, 2, 3, 4, 5, 10, 20 or 30 or more residues may be deleted.

Variants may include fragments of SEQ ID NO: 2. Such fragments retainpore forming activity. Fragments may be at least 50, at least 100, atleast 150, at least 200 or at least 250 amino acids in length. Suchfragments may be used to produce the pores. A fragment preferablycomprises the membrane spanning domain of SEQ ID NO: 2, namely K135-Q153and S183-S208.

One or more amino acids may be alternatively or additionally added tothe polypeptides described above. An extension may be provided at theamino terminal or carboxy terminal of the amino acid sequence of SEQ IDNO: 2 or polypeptide variant or fragment thereof. The extension may bequite short, for example from 1 to 10 amino acids in length.Alternatively, the extension may be longer, for example up to 50 or 100amino acids. A carrier protein may be fused to an amino acid sequenceaccording to the invention. Other fusion proteins are discussed in moredetail below.

As discussed above, a variant is a polypeptide that has an amino acidsequence which varies from that of SEQ ID NO: 2 and which retains itsability to form a pore. A variant typically contains the regions of SEQID NO: 2 that are responsible for pore formation. The pore formingability of CsgG, which contains a β-barrel, is provided by β-sheets ineach subunit. A variant of SEQ ID NO: 2 typically comprises the regionsin SEQ ID NO: 2 that form β-sheets, namely K135-Q153 and S183-S208. Oneor more modifications can be made to the regions of SEQ ID NO: 2 thatform β-sheets as long as the resulting variant retains its ability toform a pore. A variant of SEQ ID NO: 2 preferably includes one or moremodifications, such as substitutions, additions or deletions, within itsα-helices and/or loop regions.

The monomers derived from CsgG may be modified to assist theiridentification or purification, for example by the addition of astreptavidin tag or by the addition of a signal sequence to promotetheir secretion from a cell where the monomer does not naturally containsuch a sequence. Other suitable tags are discussed in more detail below.The monomer may be labelled with a revealing label. The revealing labelmay be any suitable label which allows the monomer to be detected.Suitable labels are described below.

The monomer derived from CsgG may also be produced using D-amino acids.For instance, the monomer derived from CsgG may comprise a mixture ofL-amino acids and D-amino acids. This is conventional in the art forproducing such proteins or peptides.

The monomer derived from CsgG contains one or more specificmodifications to facilitate nucleotide discrimination. The monomerderived from CsgG may also contain other non-specific modifications aslong as they do not interfere with pore formation. A number ofnon-specific side chain modifications are known in the art and may bemade to the side chains of the monomer derived from CsgG. Suchmodifications include, for example, reductive alkylation of amino acidsby reaction with an aldehyde followed by reduction with NaBH₄,amidination with methylacetimidate or acylation with acetic anhydride.

The monomer derived from CsgG can be produced using standard methodsknown in the art. The monomer derived from CsgG may be madesynthetically or by recombinant means. For example, the monomer may besynthesised by in vitro translation and transcription (IVTT). Suitablemethods for producing pores and monomers are discussed in InternationalApplication Nos. PCT/GB09/001690 (published as WO 2010/004273),PCT/GB09/001679 (published as WO 2010/004265) or PCT/GB10/000133(published as WO 2010/086603). Methods for inserting pores intomembranes are discussed.

In some embodiments, the mutant monomer is chemically modified. Themutant monomer can be chemically modified in any way and at any site.The mutant monomer is preferably chemically modified by attachment of amolecule to one or more cysteines (cysteine linkage), attachment of amolecule to one or more lysines, attachment of a molecule to one or morenon-natural amino acids, enzyme modification of an epitope ormodification of a terminus. Suitable methods for carrying out suchmodifications are well-known in the art. The mutant monomer may bechemically modified by the attachment of any molecule. For instance, themutant monomer may be chemically modified by attachment of a dye or afluorophore.

In some embodiments, the mutant monomer is chemically modified with amolecular adaptor that facilitates the interaction between a porecomprising the monomer and a target nucleotide or target polynucleotidesequence. The presence of the adaptor improves the host-guest chemistryof the pore and the nucleotide or polynucleotide sequence and therebyimproves the sequencing ability of pores formed from the mutant monomer.The principles of host-guest chemistry are well-known in the art. Theadaptor has an effect on the physical or chemical properties of the porethat improves its interaction with the nucleotide or polynucleotidesequence. The adaptor may alter the charge of the barrel or channel ofthe pore or specifically interact with or bind to the nucleotide orpolynucleotide sequence thereby facilitating its interaction with thepore.

The molecular adaptor is preferably a cyclic molecule, a cyclodextrin, aspecies that is capable of hybridization, a DNA binder or interchelator,a peptide or peptide analogue, a synthetic polymer, an aromatic planarmolecule, a small positively-charged molecule or a small moleculecapable of hydrogen-bonding.

The adaptor may be cyclic. A cyclic adaptor preferably has the samesymmetry as the pore. The adaptor preferably has eight-fold or nine-foldsymmetry since CsgG typically has eight or nine subunits around acentral axis. This is discussed in more detail below.

The adaptor typically interacts with the nucleotide or polynucleotidesequence via host-guest chemistry. The adaptor is typically capable ofinteracting with the nucleotide or polynucleotide sequence. The adaptorcomprises one or more chemical groups that are capable of interactingwith the nucleotide or polynucleotide sequence. The one or more chemicalgroups preferably interact with the nucleotide or polynucleotidesequence by non-covalent interactions, such as hydrophobic interactions,hydrogen bonding, Van der Waal's forces, n-cation interactions and/orelectrostatic forces. The one or more chemical groups that are capableof interacting with the nucleotide or polynucleotide sequence arepreferably positively charged. The one or more chemical groups that arecapable of interacting with the nucleotide or polynucleotide sequencemore preferably comprise amino groups. The amino groups can be attachedto primary, secondary or tertiary carbon atoms. The adaptor even morepreferably comprises a ring of amino groups, such as a ring of 6, 7 or 8amino groups. The adaptor most preferably comprises a ring of eightamino groups. A ring of protonated amino groups may interact withnegatively charged phosphate groups in the nucleotide or polynucleotidesequence.

The correct positioning of the adaptor within the pore can befacilitated by host-guest chemistry between the adaptor and the porecomprising the mutant monomer. The adaptor preferably comprises one ormore chemical groups that are capable of interacting with one or moreamino acids in the pore. The adaptor more preferably comprises one ormore chemical groups that are capable of interacting with one or moreamino acids in the pore via non-covalent interactions, such ashydrophobic interactions, hydrogen bonding, Van der Waal's forces,π-cation interactions and/or electrostatic forces. The chemical groupsthat are capable of interacting with one or more amino acids in the poreare typically hydroxyls or amines. The hydroxyl groups can be attachedto primary, secondary or tertiary carbon atoms. The hydroxyl groups mayform hydrogen bonds with uncharged amino acids in the pore. Any adaptorthat facilitates the interaction between the pore and the nucleotide orpolynucleotide sequence can be used.

Suitable adaptors include, but are not limited to, cyclodextrins, cyclicpeptides and cucurbiturils. The adaptor is preferably a cyclodextrin ora derivative thereof. The cyclodextrin or derivative thereof may be anyof those disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J. Am.Chem. Soc. 116, 6081-6088. The adaptor is more preferablyheptakis-6-amino-β-cyclodextrin (am₇-βCD),6-monodeoxy-6-monoamino-β-cyclodextrin (am₁-βCD) orheptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu₇-βCD). The guanidinogroup in gu₇-βCD has a much higher pKa than the primary amines inam₇-βCD and so it is more positively charged. This gu₇-βCD adaptor maybe used to increase the dwell time of the nucleotide in the pore, toincrease the accuracy of the residual current measured, as well as toincrease the base detection rate at high temperatures or low dataacquisition rates.

If a succinimidyl 3-(2-pyridyldithio)propionate (SPDP) crosslinker isused as discussed in more detail below, the adaptor is preferablyheptakis(6-deoxy-6-amino)-6-N-mono(2-pyridyl)dithiopropanoyl-β-cyclodextrin(am₆amPDP₁-βCD).

More suitable adaptors include γ-cyclodextrins, which comprise 9 sugarunits (and therefore have nine-fold symmetry). The γ-cyclodextrin maycontain a linker molecule or may be modified to comprise all or more ofthe modified sugar units used in the β-cyclodextrin examples discussedabove.

The molecular adaptor is preferably covalently attached to the mutantmonomer. The adaptor can be covalently attached to the pore using anymethod known in the art. The adaptor is typically attached via chemicallinkage. If the molecular adaptor is attached via cysteine linkage, theone or more cysteines have preferably been introduced to the mutant, forinstance in the barrel, by substitution. The mutant monomer may bechemically modified by attachment of a molecular adaptor to one or morecysteines in the mutant monomer. The one or more cysteines may benaturally-occurring, i.e. at positions 1 and/or 215 in SEQ ID NO: 2.Alternatively, the mutant monomer may be chemically modified byattachment of a molecule to one or more cysteines introduced at otherpositions. The cysteine at position 215 may be removed, for instance bysubstitution, to ensure that the molecular adaptor does not attach tothat position rather than the cysteine at position 1 or a cysteineintroduced at another position.

The reactivity of cysteine residues may be enhanced by modification ofthe adjacent residues. For instance, the basic groups of flankingarginine, histidine or lysine residues will change the pKa of thecysteines thiol group to that of the more reactive S⁻ group. Thereactivity of cysteine residues may be protected by thiol protectivegroups such as dTNB. These may be reacted with one or more cysteineresidues of the mutant monomer before a linker is attached. The moleculemay be attached directly to the mutant monomer. The molecule ispreferably attached to the mutant monomer using a linker, such as achemical crosslinker or a peptide linker.

Suitable chemical crosslinkers are well-known in the art. Preferredcrosslinkers include 2,5-dioxopyrrolidin-1-yl3-(pyridin-2-yldisulfanyl)propanoate, 2,5-dioxopyrrolidin-1-yl4-(pyridin-2-yldisulfanyl)butanoate and 2,5-dioxopyrrolidin-1-yl8-(pyridin-2-yldisulfanyl)octananoate. The most preferred crosslinker issuccinimidyl 3-(2-pyridyldithio)propionate (SPDP). Typically, themolecule is covalently attached to the bifunctional crosslinker beforethe molecule/crosslinker complex is covalently attached to the mutantmonomer but it is also possible to covalently attach the bifunctionalcrosslinker to the monomer before the bifunctional crosslinker/monomercomplex is attached to the molecule.

The linker is preferably resistant to dithiothreitol (DTT). Suitablelinkers include, but are not limited to, iodoacetamide-based andMaleimide-based linkers.

In other embodiment, the monomer may be attached to a polynucleotidebinding protein. This forms a modular sequencing system that may be usedin the methods of sequencing of the invention. Polynucleotide bindingproteins are discussed below.

The polynucleotide binding protein is preferably covalently attached tothe mutant monomer. The protein can be covalently attached to themonomer using any method known in the art. The monomer and protein maybe chemically fused or genetically fused. The monomer and protein aregenetically fused if the whole construct is expressed from a singlepolynucleotide sequence. Genetic fusion of a monomer to a polynucleotidebinding protein is discussed in International Application No.PCT/GB09/001679 (published as WO 2010/004265).

If the polynucleotide binding protein is attached via cysteine linkage,the one or more cysteines have preferably been introduced to the mutantby substitution. The one or more cysteines are preferably introducedinto loop regions which have low conservation amongst homologuesindicating that mutations or insertions may be tolerated. They aretherefore suitable for attaching a polynucleotide binding protein. Insuch embodiments, the naturally-occurring cysteine at position 251 maybe removed. The reactivity of cysteine residues may be enhanced bymodification as described above.

The polynucleotide binding protein may be attached directly to themutant monomer or via one or more linkers. The molecule may be attachedto the mutant monomer using the hybridization linkers described inInternational Application No. PCT/GB10/000132 (published as WO2010/086602). Alternatively, peptide linkers may be used. Peptidelinkers are amino acid sequences. The length, flexibility andhydrophilicity of the peptide linker are typically designed such that itdoes not to disturb the functions of the monomer and molecule. Preferredflexible peptide linkers are stretches of 2 to 20, such as 4, 6, 8, 10or 16, serine and/or glycine amino acids. More preferred flexiblelinkers include (SG)₁, (SG)₂, (SG)₃, (SG)₄, (SG)₅ and (SG)₈ wherein S isserine and G is glycine. Preferred rigid linkers are stretches of 2 to30, such as 4, 6, 8, 16 or 24, proline amino acids. More preferred rigidlinkers include (P)12 wherein P is proline.

The mutant monomer may be chemically modified with a molecular adaptorand a polynucleotide binding protein.

The molecule (with which the monomer is chemically modified) may beattached directly to the monomer or attached via a linker as disclosedin International Application Nos. PCT/GB09/001690 (published as WO2010/004273), PCT/GB09/001679 (published as WO 2010/004265) orPCT/GB10/000133 (published as WO 2010/086603).

Any of the proteins described herein, such as the mutant monomers andpores of the invention, may be modified to assist their identificationor purification, for example by the addition of histidine residues (ahis tag), aspartic acid residues (an asp tag), a streptavidin tag, aflag tag, a SUMO tag, a GST tag or a MBP tag, or by the addition of asignal sequence to promote their secretion from a cell where thepolypeptide does not naturally contain such a sequence. An alternativeto introducing a genetic tag is to chemically react a tag onto a nativeor engineered position on the protein. An example of this would be toreact a gel-shift reagent to a cysteine engineered on the outside of theprotein. This has been demonstrated as a method for separating hemolysinhetero-oligomers (Chem Biol. 1997 July; 4(7):497-505).

Any of the proteins described herein, such as the mutant monomers andpores of the invention, may be labelled with a revealing label. Therevealing label may be any suitable label which allows the protein to bedetected. Suitable labels include, but are not limited to, fluorescentmolecules, radioisotopes, e.g. ¹²⁵I, ³⁵S, enzymes, antibodies, antigens,polynucleotides and ligands such as biotin.

Any of the proteins described herein, such as the monomers or pores ofthe invention, may be made synthetically or by recombinant means. Forexample, the protein may be synthesised by in vitro translation andtranscription (IVTT). The amino acid sequence of the protein may bemodified to include non-naturally occurring amino acids or to increasethe stability of the protein. When a protein is produced by syntheticmeans, such amino acids may be introduced during production. The proteinmay also be altered following either synthetic or recombinantproduction.

Proteins may also be produced using D-amino acids. For instance, theprotein may comprise a mixture of L-amino acids and D-amino acids. Thisis conventional in the art for producing such proteins or peptides.

The protein may also contain other non-specific modifications as long asthey do not interfere with the function of the protein. A number ofnon-specific side chain modifications are known in the art and may bemade to the side chains of the protein(s). Such modifications include,for example, reductive alkylation of amino acids by reaction with analdehyde followed by reduction with NaBH₄, amidination withmethylacetimidate or acylation with acetic anhydride.

Any of the proteins described herein, including the monomers and poresof the invention, can be produced using standard methods known in theart. Polynucleotide sequences encoding a protein may be derived andreplicated using standard methods in the art. Polynucleotide sequencesencoding a protein may be expressed in a bacterial host cell usingstandard techniques in the art. The protein may be produced in a cell byin situ expression of the polypeptide from a recombinant expressionvector. The expression vector optionally carries an inducible promoterto control the expression of the polypeptide. These methods aredescribed in Sambrook, J. and Russell, D. (2001). Molecular Cloning: ALaboratory Manual, 3rd Edition. Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y.

Proteins may be produced in large scale following purification by anyprotein liquid chromatography system from protein producing organisms orafter recombinant expression. Typical protein liquid chromatographysystems include FPLC, AKTA systems, the Bio-Cad system, the Bio-RadBioLogic system and the Gilson HPLC system.

Constructs

The invention also provides a construct comprising two or morecovalently attached CsgG monomers, wherein at least one of the monomersis a mutant monomer of the invention. The construct of the inventionretains its ability to form a pore. This may be determined as discussedabove. One or more constructs of the invention may be used to form poresfor characterising, such as sequencing, polynucleotides. The constructmay comprise at least 2, at least 3, at least 4, at least 5, at least 6,at least 7, at least 8, at least 9 or at least 10 monomers. Theconstruct preferably comprises two monomers. The two or more monomersmay be the same or different.

At least one monomer in the construct is a mutant monomer of theinvention. 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 ormore, 8 or more, 9 or more or 10 or more monomers in the construct maybe mutant monomers of the invention. All of the monomers in theconstruct are preferably mutant monomers of the invention. The mutantmonomers may be the same or different. In a preferred embodiment, theconstruct comprises two mutant monomers of the invention.

The mutant monomers of the invention in the construct are preferablyapproximately the same length or are the same length. The barrels of themutant monomers of the invention in the construct are preferablyapproximately the same length or are the same length. Length may bemeasured in number of amino acids and/or units of length.

The construct may comprise one or more monomers which are not mutantmonomers of the invention. CsgG mutant monomers which are non mutantmonomers of the invention include monomers comprising SEQ ID NO: 2, 3,4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40or 41 or a comparative variant of SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 in which noneof the amino acids/positions discussed above have been been mutated. Atleast one monomer in the construct may comprise SEQ ID NO: 2, 3, 4, 5,6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41or a comparative variant of the sequence shown in SEQ ID NO: 2, 3, 4, 5,6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41.A comparative variant of SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 is at least 50%homologous to SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40 or 41 over its entire sequence based onamino acid identity. More preferably, the comparative variant may be atleast 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90% and more preferably at least 95%,97% or 99% homologous based on amino acid identity to the amino acidsequence of SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40 or 41 over the entire sequence.

The monomers in the construct are preferably genetically fused. Monomersare genetically fused if the whole construct is expressed from a singlepolynucleotide sequence. The coding sequences of the monomers may becombined in any way to form a single polynucleotide sequence encodingthe construct.

The monomers may be genetically fused in any configuration. The monomersmay be fused via their terminal amino acids. For instance, the aminoterminus of the one monomer may be fused to the carboxy terminus ofanother monomer. The second and subsequent monomers in the construct (inthe amino to carboxy direction) may comprise a methionine at their aminoterminal ends (each of which is fused to the carboxy terminus of theprevious monomer). For instance, if M is a monomer (without an aminoterminal methionine) and mM is a monomer with an amino terminalmethionine, the construct may comprise the sequence M-mM, M-mM-mM orM-mM-mM-mM. The presences of these methionines typically results fromthe expression of the start codons (i.e. ATGs) at the 5′ end of thepolynucleotides encoding the second or subsequent monomers within thepolynucleotide encoding entire construct. The first monomer in theconstruct (in the amino to carboxy direction) may also comprise amethionine (e.g. mM-mM, mM-mM-mM or mM-mM-mM-mM).

The two or more monomers may be genetically fused directly together. Themonomers are preferably genetically fused using a linker. The linker maybe designed to constrain the mobility of the monomers. Preferred linkersare amino acid sequences (i.e. peptide linkers). Any of the peptidelinkers discussed above may be used.

In another preferred embodiment, the monomers are chemically fused. Twomonomers are chemically fused if the two parts are chemically attached,for instance via a chemical crosslinker. Any of the chemicalcrosslinkers discussed above may be used. The linker may be attached toone or more cysteine residues introduced into a mutant monomer of theinvention. Alternatively, the linker may be attached to a terminus ofone of the monomers in the construct.

If a construct contains different monomers, crosslinkage of monomers tothemselves may be prevented by keeping the concentration of linker in avast excess of the monomers. Alternatively, a “lock and key” arrangementmay be used in which two linkers are used. Only one end of each linkermay react together to form a longer linker and the other ends of thelinker each react with a different monomers. Such linkers are describedin International Application No. PCT/GB10/000132 (published as WO2010/086602).

Polynucleotides

The present invention also provides polynucleotide sequences whichencode a mutant monomer of the invention. The mutant monomer may be anyof those discussed above. The polynucleotide sequence preferablycomprises a sequence at least 50%, 60%, 70%, 80%, 90% or 95% homologousbased on nucleotide identity to the sequence of SEQ ID NO: 1 over theentire sequence. There may be at least 80%, for example at least 85%,90% or 95% nucleotide identity over a stretch of 300 or more, forexample 375, 450, 525 or 600 or more, contiguous nucleotides (“hardhomology”). Homology may be calculated as described above. Thepolynucleotide sequence may comprise a sequence that differs from SEQ IDNO: 1 on the basis of the degeneracy of the genetic code.

The present invention also provides polynucleotide sequences whichencode any of the genetically fused constructs of the invention. Thepolynucleotide preferably comprises two or more variants of the sequenceshown in SEQ ID NO: 1. The polynucleotide sequence preferably comprisestwo or more sequences having at least 50%, 60%, 70%, 80%, 90% or 95%homology to SEQ ID NO: 1 based on nucleotide identity over the entiresequence. There may be at least 80%, for example at least 85%, 90% or95% nucleotide identity over a stretch of 600 or more, for example 750,900, 1050 or 1200 or more, contiguous nucleotides (“hard homology”).Homology may be calculated as described above.

Polynucleotide sequences may be derived and replicated using standardmethods in the art. Chromosomal DNA encoding wild-type CsgG may beextracted from a pore producing organism, such as Escherichia coli. Thegene encoding the pore subunit may be amplified using PCR involvingspecific primers. The amplified sequence may then undergo site-directedmutagenesis. Suitable methods of site-directed mutagenesis are known inthe art and include, for example, combine chain reaction.Polynucleotides encoding a construct of the invention can be made usingwell-known techniques, such as those described in Sambrook, J. andRussell, D. (2001). Molecular Cloning: A Laboratory Manual, 3rd Edition.Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

The resulting polynucleotide sequence may then be incorporated into arecombinant replicable vector such as a cloning vector. The vector maybe used to replicate the polynucleotide in a compatible host cell. Thuspolynucleotide sequences may be made by introducing a polynucleotideinto a replicable vector, introducing the vector into a compatible hostcell, and growing the host cell under conditions which bring aboutreplication of the vector. The vector may be recovered from the hostcell. Suitable host cells for cloning of polynucleotides are known inthe art and described in more detail below.

The polynucleotide sequence may be cloned into suitable expressionvector. In an expression vector, the polynucleotide sequence istypically operably linked to a control sequence which is capable ofproviding for the expression of the coding sequence by the host cell.Such expression vectors can be used to express a pore subunit.

The term “operably linked” refers to a juxtaposition wherein thecomponents described are in a relationship permitting them to functionin their intended manner. A control sequence “operably linked” to acoding sequence is ligated in such a way that expression of the codingsequence is achieved under conditions compatible with the controlsequences. Multiple copies of the same or different polynucleotidesequences may be introduced into the vector.

The expression vector may then be introduced into a suitable host cell.Thus, a mutant monomer or construct of the invention can be produced byinserting a polynucleotide sequence into an expression vector,introducing the vector into a compatible bacterial host cell, andgrowing the host cell under conditions which bring about expression ofthe polynucleotide sequence. The recombinantly-expressed monomer orconstruct may self-assemble into a pore in the host cell membrane.Alternatively, the recombinant pore produced in this manner may beremoved from the host cell and inserted into another membrane. Whenproducing pores comprising at least two different monomers orconstructs, the different monomers or constructs may be expressedseparately in different host cells as described above, removed from thehost cells and assembled into a pore in a separate membrane, such as arabbit cell membrane or a synthetic membrane.

The vectors may be for example, plasmid, virus or phage vectors providedwith an origin of replication, optionally a promoter for the expressionof the said polynucleotide sequence and optionally a regulator of thepromoter. The vectors may contain one or more selectable marker genes,for example a tetracycline resistance gene. Promoters and otherexpression regulation signals may be selected to be compatible with thehost cell for which the expression vector is designed. A T7, trc, lac,ara or λ_(L) promoter is typically used.

The host cell typically expresses the monomer or construct at a highlevel. Host cells transformed with a polynucleotide sequence will bechosen to be compatible with the expression vector used to transform thecell. The host cell is typically bacterial and preferably Escherichiacoli. Any cell with a λ DE3 lysogen, for example C41 (DE3), BL21 (DE3),JM109 (DE3), B834 (DE3), TUNER, Origami and Origami B, can express avector comprising the T7 promoter. In addition to the conditions listedabove any of the methods cited in Cao et al, 2014, PNAS, Structure ofthe nonameric bacterial amyloid secretion channel, doi-1411942111 andGoyal et al, 2014, Nature, 516, 250-253 structural and mechanisticinsights into the bacterial amyloid secretion channel CsgG may be usedto express the CsgG proteins.

The invention also comprises a method of producing a mutant monomer ofthe invention or a construct of the invention. The method comprisesexpressing a polynucleotide of the invention in a suitable host cell.The polynucleotide is preferably part of a vector and is preferablyoperably linked to a promoter.

Pores

The invention also provides various pores. The pores of the inventionare ideal for characterising, such as sequencing, polynucleotidesequences because they can discriminate between different nucleotideswith a high degree of sensitivity. The pores can surprisinglydistinguish between the four nucleotides in DNA and RNA. The pores ofthe invention can even distinguish between methylated and unmethylatednucleotides. The base resolution of pores of the invention issurprisingly high. The pores show almost complete separation of all fourDNA nucleotides. The pores further discriminate between deoxycytidinemonophosphate (dCMP) and methyl-dCMP based on the dwell time in the poreand the current flowing through the pore.

The pores of the invention can also discriminate between differentnucleotides under a range of conditions. In particular, the pores willdiscriminate between nucleotides under conditions that are favourable tothe characterising, such as sequencing, of nucleic acids. The extent towhich the pores of the invention can discriminate between differentnucleotides can be controlled by altering the applied potential, thesalt concentration, the buffer, the temperature and the presence ofadditives, such as urea, betaine and DTT. This allows the function ofthe pores to be fine-tuned, particularly when sequencing. This isdiscussed in more detail below. The pores of the invention may also beused to identify polynucleotide polymers from the interaction with oneor more monomers rather than on a nucleotide by nucleotide basis.

A pore of the invention may be isolated, substantially isolated,purified or substantially purified. A pore of the invention is isolatedor purified if it is completely free of any other components, such aslipids or other pores. A pore is substantially isolated if it is mixedwith carriers or diluents which will not interfere with its intendeduse. For instance, a pore is substantially isolated or substantiallypurified if it is present in a form that comprises less than 10%, lessthan 5%, less than 2% or less than 1% of other components, such astriblock copolymers, lipids or other pores. Alternatively, a pore of theinvention may be present in a membrane. Suitable membranes are discussedbelow.

A pore of the invention may be present as an individual or single pore.Alternatively, a pore of the invention may be present in a homologous orheterologous population of two or more pores.

Homo-Oligomeric Pores

The invention also provides a homo-oligomeric pore derived from CsgGcomprising identical mutant monomers of the invention. Thehomo-oligomeric pore may comprise any of the mutants of the invention.The homo-oligomeric pore of the invention is ideal for characterising,such as sequencing, polynucleotides. The homo-oligomeric pore of theinvention may have any of the advantages discussed above.

The homo-oligomeric pore may contain any number of mutant monomers. Thepore typically comprises at least 7, at least 8, at least 9 or at least10 identical mutant monomers, such as 7, 8, 9 or 10 mutant monomers. Thepore preferably comprises eight or nine identical mutant monomers. Oneor more, such as 2, 3, 4, 5, 6, 7, 8, 9 or 10, of the mutant monomers ispreferably chemically modified as discussed above.

Methods for making pores are discussed in more detail below.

Hetero-Oligomeric Pores

The invention also provides a hetero-oligomeric pore derived from CsgGcomprising at least one mutant monomer of the invention. Thehetero-oligomeric pore of the invention is ideal for characterising,such as sequencing, polynucleotides. Hetero-oligomeric pores can be madeusing methods known in the art (e.g. Protein Sci. 2002 July;11(7):1813-24).

The hetero-oligomeric pore contains sufficient monomers to form thepore. The monomers may be of any type. The pore typically comprises atleast 7, at least 8, at least 9 or at least 10 monomers, such as 7, 8, 9or 10 monomers. The pore preferably comprises eight or nine monomers.

In a preferred embodiment, all of the monomers (such as 10, 9, 8 or 7 ofthe monomers) are mutant monomers of the invention and at least one ofthem differs from the others. In a more preferred embodiment, the porecomprises eight or nine mutant monomers of the invention and at leastone of them differs from the others. They may all differ from oneanother.

The mutant monomers of the invention in the pore are preferablyapproximately the same length or are the same length. The barrels of themutant monomers of the invention in the pore are preferablyapproximately the same length or are the same length. Length may bemeasured in number of amino acids and/or units of length.

In another preferred embodiment, at least one of the mutant monomers isnot a mutant monomer of the invention. In this embodiment, the remainingmonomers are preferably mutant monomers of the invention. Hence, thepore may comprise 9, 8, 7, 6, 5, 4, 3, 2 or 1 mutant monomers of theinvention. Any number of the monomers in the pore may not be a mutantmonomer of the invention. The pore preferably comprises seven or eightmutant monomers of the invention and a monomer which is not a monomer ofthe invention. The mutant monomers of the invention may be the same ordifferent.

The mutant monomers of the invention in the construct are preferablyapproximately the same length or are the same length. The barrels of themutant monomers of the invention in the construct are preferablyapproximately the same length or are the same length. Length may bemeasured in number of amino acids and/or units of length.

The pore may comprise one or more monomers which are not mutant monomersof the invention. CsgG monomers which are not mutant monomers of theinvention include monomers comprising SEQ ID NO: 2, 3, 4, 5, 6, 7, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 or acomparative variant of SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 in which none of the aminoacids/positions discussed above in relation to the invention have beenmutated/substituted. A comparative variant of SEQ ID NO: 2, 3, 4, 5, 6,7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 istypically at least 50% homologous to SEQ ID NO: 2, 3, 4, 5, 6, 7, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 over itsentire sequence based on amino acid identity. More preferably, thecomparative variant may be at least 55%, at least 60%, at least 65%, atleast 70%, at least 75%, at least 80%, at least 85%, at least 90% andmore preferably at least 95%, 97% or 99% homologous based on amino acididentity to the amino acid sequence of SEQ ID NO: 2, 3, 4, 5, 6, 7, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 over theentire sequence.

In all the embodiments discussed above, one or more, such as 2, 3, 4, 5,6, 7, 8, 9 or 10, of the mutant monomers is preferably chemicallymodified as discussed above.

Methods for making pores are discussed in more detail below.

Construct-Containing Pores

The invention also provides a pore comprising at least one construct ofthe invention. A construct of the invention comprises two or morecovalently attached monomers derived from CsgG wherein at least one ofthe monomers is a mutant monomer of the invention. In other words, aconstruct must contain more than one monomer. The pore containssufficient constructs and, if necessary, monomers to form the pore. Forinstance, an octameric pore may comprise (a) four constructs eachcomprising two constructs, (b) two constructs each comprising fourmonomers or (b) one construct comprising two monomers and six monomersthat do not form part of a construct. For instance, an nonameric poremay comprise (a) four constructs each comprising two constructs and onemonomer that does not form part of a construct, (b) two constructs eachcomprising four monomers and a monomer that does not form part of aconstruct or (b) one construct comprising two monomers and sevenmonomers that do not form part of a construct. Other combinations ofconstructs and monomers can be envisaged by the skilled person.

At least two of the monomers in the pore are in the form of a constructof the invention. The construct, and hence the pore, comprises at leastone mutant monomer of the invention. The pore typically comprises atleast 7, at least 8, at least 9 or at least 10 monomers, such as 7, 8, 9or 10 monomers, in total (at least two of which must be in a construct).The pore preferably comprises eight or nine monomers (at least two ofwhich must be in a construct).

The construct containing pore may be a homo-oligomer (i.e. includeidentical constructs) or be a hetero-oligomer (i.e. where at least oneconstruct differs from the others).

A pore typically contains (a) one construct comprising two monomers and(b) 5, 6, 7 or 8 monomers. The construct may be any of those discussedabove. The monomers may be any of those discussed above, includingmutant monomers of the invention, monomers comprising SEQ ID NO: 2, 3,4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40or 41 and mutant monomers comprising a comparative variant of SEQ ID NO:2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40 or 41 as discussed above.

Another typical pore comprises more than one construct of the invention,such as two, three or four constructs of the invention. If necessary,such pores further comprise sufficient additional monomers or constructsto form the pore. The additional monomer(s) may be any of thosediscussed above, including mutant monomers of the invention, monomerscomprising SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40 or 41 and mutant monomers comprising acomparative variant of SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 as discussed above. Theadditional construct(s) may be any of those discussed above or may be aconstruct comprising two or more covalently attached CsgG monomers eachcomprising a monomer comprising SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 or a comparativevariant of SEQ ID NO: 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40 or 41 as discussed above.

A further pore of the invention comprises only constructs comprising 2monomers, for example a pore may comprise 4, 5, 6, 7 or 8 constructscomprising 2 monomers. At least one construct is a construct of theinvention, i.e. at least one monomer in the at least one construct, andpreferably each monomer in the at least one construct, is a mutantmonomer of the invention. All of the constructs comprising 2 monomersmay be constructs of the invention.

A specific pore according to the invention comprises four constructs ofthe invention each comprising two monomers, wherein at least one monomerin each construct, and preferably each monomer in each construct, is amutant monomer of the invention. The constructs may oligomerise into apore with a structure such that only one monomer of each constructcontributes to the channel of the pore. Typically the other monomers ofthe construct will be on the outside of the channel of the pore. Forexample, pores of the invention may comprise 7, 8, 9 or 10 constructscomprising 2 monomers where the channel comprises 7, 8, 9 or 10monomers.

Mutations can be introduced into the construct as described above. Themutations may be alternating, i.e. the mutations are different for eachmonomer within a two monomer construct and the constructs are assembledas a homo-oligomer resulting in alternating modifications. In otherwords, monomers comprising MutA and MutB are fused and assembled to forman A-B:A-B:A-B:A-B pore. Alternatively, the mutations may beneighbouring, i.e. identical mutations are introduced into two monomersin a construct and this is then oligomerised with different mutantmonomers or constructs. In other words, monomers comprising MutA arefused follow by oligomerisation with MutB-containing monomers to formA-A:B:B:B:B:B:B.

One or more of the monomers of the invention in a construct-containingpore may be chemically-modified as discussed above.

Analyte Characterisation

The invention provides a method of determining the presence, absence orone or more characteristics of a target analyte. The method involvescontacting the target analyte with a pore of the invention such that thetarget analyte moves with respect to, such as through, the pore andtaking one or more measurements as the analyte moves with respect to thepore and thereby determining the presence, absence or one or morecharacteristics of the analyte. The target analyte may also be calledthe template analyte or the analyte of interest.

Steps (a) and (b) are preferably carried out with a potential appliedacross the pore. As discussed in more detail below, the appliedpotential typically results in the formation of a complex between thepore and a polynucleotide binding protein. The applied potential may bea voltage potential. Alternatively, the applied potential may be achemical potential. An example of this is using a salt gradient acrossan amphiphilic layer. A salt gradient is disclosed in Holden et al., JAm Chem Soc. 2007 Jul. 11; 129(27):8650-5.

The method is for determining the presence, absence or one or morecharacteristics of a target analyte. The method may be for determiningthe presence, absence or one or more characteristics of at least oneanalyte. The method may concern determining the presence, absence or oneor more characteristics of two or more analytes. The method may comprisedetermining the presence, absence or one or more characteristics of anynumber of analytes, such as 2, 5, 10, 15, 20, 30, 40, 50, 100 or moreanalytes. Any number of characteristics of the one or more analytes maybe determined, such as 1, 2, 3, 4, 5, 10 or more characteristics.

The target analyte is preferably a metal ion, an inorganic salt, apolymer, an amino acid, a peptide, a polypeptide, a protein, anucleotide, an oligonucleotide, a polynucleotide, a dye, a bleach, apharmaceutical, a diagnostic agent, a recreational drug, an explosive oran environmental pollutant. The method may concern determining thepresence, absence or one or more characteristics of two or more analytesof the same type, such as two or more proteins, two or more nucleotidesor two or more pharmaceuticals. Alternatively, the method may concerndetermining the presence, absence or one or more characteristics of twoor more analytes of different types, such as one or more proteins, oneor more nucleotides and one or more pharmaceuticals.

The target analyte can be secreted from cells. Alternatively, the targetanalyte can be an analyte that is present inside cells such that theanalyte must be extracted from the cells before the invention can becarried out.

The analyte is preferably an amino acid, a peptide, a polypeptidesand/or a protein. The amino acid, peptide, polypeptide or protein can benaturally-occurring or non-naturally-occurring. The polypeptide orprotein can include within them synthetic or modified amino acids. Anumber of different types of modification to amino acids are known inthe art. Suitable amino acids and modifications thereof are above. Forthe purposes of the invention, it is to be understood that the targetanalyte can be modified by any method available in the art.

The protein can be an enzyme, an antibody, a hormone, a growth factor ora growth regulatory protein, such as a cytokine. The cytokine may beselected from interleukins, preferably IFN-1, IL-1, IL-2, IL-4, IL-5,IL-6, IL-10, IL-12 and IL-13, interferons, preferably IL-γ, and othercytokines such as TNF-α. The protein may be a bacterial protein, afungal protein, a virus protein or a parasite-derived protein.

The target analyte is preferably a nucleotide, an oligonucleotide or apolynucleotide. Nucleotides and polynucleotides are discussed below.Oligonucleotides are short nucleotide polymers which typically have 50or fewer nucleotides, such 40 or fewer, 30 or fewer, 20 or fewer, 10 orfewer or 5 or fewer nucleotides. The oligonucleotides may comprise anyof the nucleotides discussed below, including the abasic and modifiednucleotides.

The target analyte, such as a target polynucleotide, may be present inany of the suitable samples discussed below.

The pore is typically present in a membrane as discussed below. Thetarget analyte may be coupled or delivered to the membrane using of themethods discussed below.

Any of the measurements discussed below can be used to determine thepresence, absence or one or more characteristics of the target analyte.The method preferably comprises contacting the target analyte with thepore such that the analyte moves with respect to, such as moves through,the pore and measuring the current passing through the pore as theanalyte moves with respect to the pore and thereby determining thepresence, absence or one or more characteristics of the analyte.

The target analyte is present if the current flows through the pore in amanner specific for the analyte (i.e. if a distinctive currentassociated with the analyte is detected flowing through the pore). Theanalyte is absent if the current does not flow through the pore in amanner specific for the nucleotide. Control experiments can be carriedout in the presence of the analyte to determine the way in which ifaffects the current flowing through the pore.

The invention can be used to differentiate analytes of similar structureon the basis of the different effects they have on the current passingthrough a pore. Individual analytes can be identified at the singlemolecule level from their current amplitude when they interact with thepore. The invention can also be used to determine whether or not aparticular analyte is present in a sample. The invention can also beused to measure the concentration of a particular analyte in a sample.Analyte characterisation using pores other than CsgG is known in theart.

Polynucleotide Characterisation

The invention provides a method of characterising a targetpolynucleotide, such as sequencing a polynucleotide. There are two mainstrategies for characterising or sequencing polynucleotides usingnanopores, namely strand characterisation/sequencing and exonucleasecharacterisation/sequencing. The method of the invention may concerneither method.

In strand sequencing, the DNA is translocated through the nanoporeeither with or against an applied potential. Exonucleases that actprogressively or processively on double stranded DNA can be used on thecis side of the pore to feed the remaining single strand through underan applied potential or the trans side under a reverse potential.Likewise, a helicase that unwinds the double stranded DNA can also beused in a similar manner. A polymerase may also be used. There are alsopossibilities for sequencing applications that require strandtranslocation against an applied potential, but the DNA must be first“caught” by the enzyme under a reverse or no potential. With thepotential then switched back following binding the strand will pass cisto trans through the pore and be held in an extended conformation by thecurrent flow. The single strand DNA exonucleases or single strand DNAdependent polymerases can act as molecular motors to pull the recentlytranslocated single strand back through the pore in a controlledstepwise manner, trans to cis, against the applied potential.

In one embodiment, the method of characterising a target polynucleotideinvolves contacting the target sequence with a pore of the invention anda helicase enzyme. Any helicase may be used in the method. Suitablehelicases are discussed below. Helicases may work in two modes withrespect to the pore. First, the method is preferably carried out using ahelicase such that it controls movement of the target sequence throughthe pore with the field resulting from the applied voltage. In this modethe 5′ end of the DNA is first captured in the pore, and the enzymecontrols movement of the DNA into the pore such that the target sequenceis passed through the pore with the field until it finally translocatesthrough to the trans side of the bilayer. Alternatively, the method ispreferably carried out such that a helicase enzyme controls movement ofthe target sequence through the pore against the field resulting fromthe applied voltage. In this mode the 3′ end of the DNA is firstcaptured in the pore, and the enzyme controls movement of the DNAthrough the pore such that the target sequence is pulled out of the poreagainst the applied field until finally ejected back to the cis side ofthe bilayer.

In exonuclease sequencing, an exonuclease releases individualnucleotides from one end of the target polynucleotide and theseindividual nucleotides are identified as discussed below. In anotherembodiment, the method of characterising a target polynucleotideinvolves contacting the target sequence with a pore and an exonucleaseenzyme. Any of the exonuclease enzymes discussed below may be used inthe method. The enzyme may be covalently attached to the pore asdiscussed below.

Exonucleases are enzymes that typically latch onto one end of apolynucleotide and digest the sequence one nucleotide at a time fromthat end. The exonuclease can digest the polynucleotide in the 5′ to 3′direction or 3′ to 5′ direction. The end of the polynucleotide to whichthe exonuclease binds is typically determined through the choice ofenzyme used and/or using methods known in the art. Hydroxyl groups orcap structures at either end of the polynucleotide may typically be usedto prevent or facilitate the binding of the exonuclease to a particularend of the polynucleotide.

The method involves contacting the polynucleotide with the exonucleaseso that the nucleotides are digested from the end of the polynucleotideat a rate that allows characterisation or identification of a proportionof nucleotides as discussed above. Methods for doing this are well knownin the art. For example, Edman degradation is used to successivelydigest single amino acids from the end of polypeptide such that they maybe identified using High Performance Liquid Chromatography (HPLC). Ahomologous method may be used in the present invention.

The rate at which the exonuclease functions is typically slower than theoptimal rate of a wild-type exonuclease. A suitable rate of activity ofthe exonuclease in the method of the invention involves digestion offrom 0.5 to 1000 nucleotides per second, from 0.6 to 500 nucleotides persecond, 0.7 to 200 nucleotides per second, from 0.8 to 100 nucleotidesper second, from 0.9 to 50 nucleotides per second or 1 to 20 or 10nucleotides per second. The rate is preferably 1, 10, 100, 500 or 1000nucleotides per second. A suitable rate of exonuclease activity can beachieved in various ways. For example, variant exonucleases with areduced optimal rate of activity may be used in accordance with theinvention.

In the strand characterisation embodiment, the method comprisescontacting the polynucleotide with a pore of the invention such that thepolynucleotide moves with respect to, such as through, the pore andtaking one or more measurements as the polynucleotide moves with respectto the pore, wherein the measurements are indicative of one or morecharacteristics of the polynucleotide, and thereby characterising thetarget polynucleotide.

In the exonucleotide characterisation embodiment, the method comprisescontacting the polynucleotide with a pore of the invention and anexonucleoase such that the exonuclease digests individual nucleotidesfrom one end of the target polynucleotide and the individual nucleotidesmove with respect to, such as through, the pore and taking one or moremeasurements as the individual nucleotides move with respect to thepore, wherein the measurements are indicative of one or morecharacteristics of the individual nucleotides, and therebycharacterising the target polynucleotide.

An individual nucleotide is a single nucleotide. An individualnucleotide is one which is not bound to another nucleotide orpolynucleotide by a nucleotide bond. A nucleotide bond involves one ofthe phosphate groups of a nucleotide being bound to the sugar group ofanother nucleotide. An individual nucleotide is typically one which isnot bound by a nucleotide bond to another polynucleotide of at least 5,at least 10, at least 20, at least 50, at least 100, at least 200, atleast 500, at least 1000 or at least 5000 nucleotides. For example, theindividual nucleotide has been digested from a target polynucleotidesequence, such as a DNA or RNA strand. The nucleotide can be any ofthose discussed below.

The individual nucleotides may interact with the pore in any manner andat any site. The nucleotides preferably reversibly bind to the pore viaor in conjunction with an adaptor as discussed above. The nucleotidesmost preferably reversibly bind to the pore via or in conjunction withthe adaptor as they pass through the pore across the membrane. Thenucleotides can also reversibly bind to the barrel or channel of thepore via or in conjunction with the adaptor as they pass through thepore across the membrane.

During the interaction between the individual nucleotide and the pore,the nucleotide typically affects the current flowing through the pore ina manner specific for that nucleotide. For example, a particularnucleotide will reduce the current flowing through the pore for aparticular mean time period and to a particular extent. In other words,the current flowing through the pore is distinctive for a particularnucleotide. Control experiments may be carried out to determine theeffect a particular nucleotide has on the current flowing through thepore. Results from carrying out the method of the invention on a testsample can then be compared with those derived from such a controlexperiment in order to identify a particular nucleotide in the sample ordetermine whether a particular nucleotide is present in the sample. Thefrequency at which the current flowing through the pore is affected in amanner indicative of a particular nucleotide can be used to determinethe concentration of that nucleotide in the sample. The ratio ofdifferent nucleotides within a sample can also be calculated. Forinstance, the ratio of dCMP to methyl-dCMP can be calculated.

The method involves measuring one or more characteristics of the targetpolynucleotide. The target polynucleotide may also be called thetemplate polynucleotide or the polynucleotide of interest.

This embodiment also uses a pore of the invention. Any of the pores andembodiments discussed above with reference to the target analyte may beused.

Polynucleotide

A polynucleotide, such as a nucleic acid, is a macromolecule comprisingtwo or more nucleotides. The polynucleotide or nucleic acid may compriseany combination of any nucleotides. The nucleotides can be naturallyoccurring or artificial. One or more nucleotides in the polynucleotidecan be oxidized or methylated. One or more nucleotides in thepolynucleotide may be damaged. For instance, the polynucleotide maycomprise a pyrimidine dimer. Such dimers are typically associated withdamage by ultraviolet light and are the primary cause of skin melanomas.One or more nucleotides in the polynucleotide may be modified, forinstance with a label or a tag. Suitable labels are described below. Thepolynucleotide may comprise one or more spacers.

A nucleotide typically contains a nucleobase, a sugar and at least onephosphate group. The nucleobase and sugar form a nucleoside.

The nucleobase is typically heterocyclic. Nucleobases include, but arenot limited to, purines and pyrimidines and more specifically adenine(A), guanine (G), thymine (T), uracil (U) and cytosine (C).

The sugar is typically a pentose sugar. Nucleotide sugars include, butare not limited to, ribose and deoxyribose. The sugar is preferably adeoxyribose.

The polynucleotide preferably comprises the following nucleosides:deoxyadenosine (dA), deoxyuridine (dU) and/or thymidine (dT),deoxyguanosine (dG) and deoxycytidine (dC).

The nucleotide is typically a ribonucleotide or deoxyribonucleotide. Thenucleotide typically contains a monophosphate, diphosphate ortriphosphate. The nucleotide may comprise more than three phosphates,such as 4 or 5 phosphates. Phosphates may be attached on the 5′ or 3′side of a nucleotide. Nucleotides include, but are not limited to,adenosine monophosphate (AMP), guanosine monophosphate (GMP), thymidinemonophosphate (TMP), uridine monophosphate (UMP), 5-methylcytidinemonophosphate, 5-hydroxymethylcytidine monophosphate, cytidinemonophosphate (CMP), cyclic adenosine monophosphate (cAMP), cyclicguanosine monophosphate (cGMP), deoxyadenosine monophosphate (dAMP),deoxyguanosine monophosphate (dGMP), deoxythymidine monophosphate(dTMP), deoxyuridine monophosphate (dUMP), deoxycytidine monophosphate(dCMP) and deoxymethylcytidine monophosphate. The nucleotides arepreferably selected from AMP, TMP, GMP, CMP, UMP, dAMP, dTMP, dGMP, dCMPand dUMP.

A nucleotide may be abasic (i.e. lack a nucleobase). A nucleotide mayalso lack a nucleobase and a sugar (i.e. is a C3 spacer).

The nucleotides in the polynucleotide may be attached to each other inany manner. The nucleotides are typically attached by their sugar andphosphate groups as in nucleic acids. The nucleotides may be connectedvia their nucleobases as in pyrimidine dimers.

The polynucleotide may be single stranded or double stranded. Thepolynucleotide is preferably single stranded. Single strandedpolynucleotide characterization is referred to as 1D in the Examples. Atleast a portion of the polynucleotide may be double stranded.

The polynucleotide can be a nucleic acid, such as deoxyribonucleic acid(DNA) or ribonucleic acid (RNA). The polynucleotide can comprise onestrand of RNA hybridised to one strand of DNA. The polynucleotide may beany synthetic nucleic acid known in the art, such as peptide nucleicacid (PNA), glycerol nucleic acid (GNA), threose nucleic acid (TNA),locked nucleic acid (LNA) or other synthetic polymers with nucleotideside chains. The PNA backbone is composed of repeatingN-(2-aminoethyl)-glycine units linked by peptide bonds. The GNA backboneis composed of repeating glycol units linked by phosphodiester bonds.The TNA backbone is composed of repeating threose sugars linked togetherby phosphodiester bonds. LNA is formed from ribonucleotides as discussedabove having an extra bridge connecting the 2′ oxygen and 4′ carbon inthe ribose moiety. Bridged nucleic acids (BNAs) are modified RNAnucleotides. They may also be called constrained or inaccessible RNA.BNA monomers can contain a five-membered, six-membered or even aseven-membered bridged structure with a “fixed” C3′-endo sugarpuckering. The bridge is synthetically incorporated at the 2′,4′-position of the ribose to produce a 2′, 4′-BNA monomer.

The polynucleotide is most preferably ribonucleic nucleic acid (RNA) ordeoxyribonucleic acid (DNA).

The polynucleotide can be any length. For example, the polynucleotidecan be at least 10, at least 50, at least 100, at least 150, at least200, at least 250, at least 300, at least 400 or at least 500nucleotides or nucleotide pairs in length. The polynucleotide can be1000 or more nucleotides or nucleotide pairs, 5000 or more nucleotidesor nucleotide pairs in length or 100000 or more nucleotides ornucleotide pairs in length.

Any number of polynucleotides can be investigated. For instance, themethod of the invention may concern characterising 2, 3, 4, 5, 6, 7, 8,9, 10, 20, 30, 50, 100 or more polynucleotides. If two or morepolynucleotides are characterised, they may be different polynucleotidesor two instances of the same polynucleotide.

The polynucleotide can be naturally occurring or artificial. Forinstance, the method may be used to verify the sequence of amanufactured oligonucleotide. The method is typically carried out invitro.

Sample

The polynucleotide is typically present in any suitable sample. Theinvention is typically carried out on a sample that is known to containor suspected to contain the polynucleotide. Alternatively, the inventionmay be carried out on a sample to confirm the identity of apolynucleotide whose presence in the sample is known or expected.

The sample may be a biological sample. The invention may be carried outin vitro using a sample obtained from or extracted from any organism ormicroorganism. The organism or microorganism is typically archaeal,prokaryotic or eukaryotic and typically belongs to one of the fivekingdoms: plantae, animalia, fungi, monera and protista. The inventionmay be carried out in vitro on a sample obtained from or extracted fromany virus. The sample is preferably a fluid sample. The sample typicallycomprises a body fluid of the patient. The sample may be urine, lymph,saliva, mucus or amniotic fluid but is preferably blood, plasma orserum.

Typically, the sample is human in origin, but alternatively it may befrom another mammal animal such as from commercially farmed animals suchas horses, cattle, sheep, fish, chickens or pigs or may alternatively bepets such as cats or dogs. Alternatively, the sample may be of plantorigin, such as a sample obtained from a commercial crop, such as acereal, legume, fruit or vegetable, for example wheat, barley, oats,canola, maize, soya, rice, rhubarb, bananas, apples, tomatoes, potatoes,grapes, tobacco, beans, lentils, sugar cane, cocoa, cotton.

The sample may be a non-biological sample. The non-biological sample ispreferably a fluid sample. Examples of non-biological samples includesurgical fluids, water such as drinking water, sea water or river water,and reagents for laboratory tests.

The sample is typically processed prior to being used in the invention,for example by centrifugation or by passage through a membrane thatfilters out unwanted molecules or cells, such as red blood cells. Themay be measured immediately upon being taken. The sample may also betypically stored prior to assay, preferably below −70° C.

Characterisation

The method may involve measuring two, three, four or five or morecharacteristics of the polynucleotide. The one or more characteristicsare preferably selected from (i) the length of the polynucleotide, (ii)the identity of the polynucleotide, (iii) the sequence of thepolynucleotide, (iv) the secondary structure of the polynucleotide and(v) whether or not the polynucleotide is modified. Any combination of(i) to (v) may be measured in accordance with the invention, such as{i}, {ii}, {iii}, {iv}, {v}, {i,ii}, {i,iii}, {i,iv}, {i,v}, {ii,iii},{ii,iv}, {ii,v}, {iii,iv}, {iii,v}, {iv,v}, {i,ii,iii}, {i,ii,iv},{i,ii,v}, {i,iii,iv}, {iii,v}, {i,iv,v}, {ii,iii,iv}, {ii,iii,v},{ii,iv,v}, {iii,iv,v}, {i,ii,iii,iv}, {i,ii,iii,v}, {i,ii,iv,v},{i,iii,iv,v}, {ii,iii,iv,v} or {i,ii,iii,iv,v}. Different combinationsof (i) to (v) may be measured for the first polynucleotide compared withthe second polynucleotide, including any of those combinations listedabove.

For (i), the length of the polynucleotide may be measured for example bydetermining the number of interactions between the polynucleotide andthe pore or the duration of interaction between the polynucleotide andthe pore.

For (ii), the identity of the polynucleotide may be measured in a numberof ways. The identity of the polynucleotide may be measured inconjunction with measurement of the sequence of the polynucleotide orwithout measurement of the sequence of the polynucleotide. The former isstraightforward; the polynucleotide is sequenced and thereby identified.The latter may be done in several ways. For instance, the presence of aparticular motif in the polynucleotide may be measured (withoutmeasuring the remaining sequence of the polynucleotide). Alternatively,the measurement of a particular electrical and/or optical signal in themethod may identify the polynucleotide as coming from a particularsource.

For (iii), the sequence of the polynucleotide can be determined asdescribed previously. Suitable sequencing methods, particularly thoseusing electrical measurements, are described in Stoddart D et al., ProcNatl Acad Sci, 12; 106(19):7702-7, Lieberman K R et al, J Am Chem Soc.2010; 132(50):17961-72, and International Application WO 2000/28312.

For (iv), the secondary structure may be measured in a variety of ways.For instance, if the method involves an electrical measurement, thesecondary structure may be measured using a change in dwell time or achange in current flowing through the pore. This allows regions ofsingle-stranded and double-stranded polynucleotide to be distinguished.

For (v), the presence or absence of any modification may be measured.The method preferably comprises determining whether or not thepolynucleotide is modified by methylation, by oxidation, by damage, withone or more proteins or with one or more labels, tags or spacers.Specific modifications will result in specific interactions with thepore which can be measured using the methods described below. Forinstance, methylcyotsine may be distinguished from cytosine on the basisof the current flowing through the pore during its interaction with eachnucleotide.

The target polynucleotide is contacted with a a pore of the invention.The pore is typically present in a membrane. Suitable membranes arediscussed below. The method may be carried out using any apparatus thatis suitable for investigating a membrane/pore system in which a pore ispresent in a membrane. The method may be carried out using any apparatusthat is suitable for transmembrane pore sensing. For example, theapparatus comprises a chamber comprising an aqueous solution and abarrier that separates the chamber into two sections. The barriertypically has an aperture in which the membrane containing the pore isformed. Alternatively the barrier forms the membrane in which the poreis present.

The method may be carried out using the apparatus described inInternational Application No. PCT/GB08/000562 (WO 2008/102120).

A variety of different types of measurements may be made. This includeswithout limitation: electrical measurements and optical measurements.Possible electrical measurements include: current measurements,impedance measurements, tunnelling measurements (Ivanov A P et al., NanoLett. 2011 Jan. 12; 11(1):279-85), and FET measurements (InternationalApplication WO 2005/124888). Optical measurements may be combined withelectrical measurements (Soni G V et al., Rev Sci Instrum. 2010 January;81(1):014301). The measurement may be a transmembrane currentmeasurement such as measurement of ionic current flowing through thepore.

Electrical measurements may be made using standard single channelrecording equipment as describe in Stoddart D et al., Proc Natl AcadSci, 12; 106(19):7702-7, Lieberman K R et al, J Am Chem Soc. 2010;132(50):17961-72, and International Application WO 2000/28312.Alternatively, electrical measurements may be made using a multi-channelsystem, for example as described in International Application WO2009/077734 and International Application WO 2011/067559.

The method is preferably carried out with a potential applied across themembrane. The applied potential may be a voltage potential.Alternatively, the applied potential may be a chemical potential. Anexample of this is using a salt gradient across a membrane, such as anamphiphilic layer. A salt gradient is disclosed in Holden et al., J AmChem Soc. 2007 Jul. 11; 129(27):8650-5. In some instances, the currentpassing through the pore as a polynucleotide moves with respect to thepore is used to estimate or determine the sequence of thepolynucleotide. This is strand sequencing.

The method may involve measuring the current passing through the pore asthe polynucleotide moves with respect to the pore. Therefore theapparatus used in the method may also comprise an electrical circuitcapable of applying a potential and measuring an electrical signalacross the membrane and pore. The methods may be carried out using apatch clamp or a voltage clamp. The methods preferably involve the useof a voltage clamp.

The method of the invention may involve the measuring of a currentpassing through the pore as the polynucleotide moves with respect to thepore. Suitable conditions for measuring ionic currents throughtransmembrane protein pores are known in the art and disclosed in theExample. The method is typically carried out with a voltage appliedacross the membrane and pore. The voltage used is typically from +5 V to−5 V, such as from +4 V to −4 V, +3 V to −3 V or +2 V to −2 V. Thevoltage used is typically from −600 mV to +600 mV or −400 mV to +400 mV.The voltage used is preferably in a range having a lower limit selectedfrom −400 mV, −300 mV, −200 mV, −150 mV, −100 mV, −50 mV, −20 mV and 0mV and an upper limit independently selected from +10 mV, +20 mV, +50mV, +100 mV, +150 mV, +200 mV, +300 mV and +400 mV. The voltage used ismore preferably in the range 100 mV to 240 mV and most preferably in therange of 120 mV to 220 mV. It is possible to increase discriminationbetween different nucleotides by a pore by using an increased appliedpotential.

The method is typically carried out in the presence of any chargecarriers, such as metal salts, for example alkali metal salt, halidesalts, for example chloride salts, such as alkali metal chloride salt.Charge carriers may include ionic liquids or organic salts, for exampletetramethyl ammonium chloride, trimethylphenyl ammonium chloride,phenyltrimethyl ammonium chloride, or 1-ethyl-3-methyl imidazoliumchloride. In the exemplary apparatus discussed above, the salt ispresent in the aqueous solution in the chamber. Potassium chloride(KCl), sodium chloride (NaCl), caesium chloride (CsCl) or a mixture ofpotassium ferrocyanide and potassium ferricyanide is typically used.KCl, NaCl and a mixture of potassium ferrocyanide and potassiumferricyanide are preferred. The charge carriers may be asymmetric acrossthe membrane. For instance, the type and/or concentration of the chargecarriers may be different on each side of the membrane.

The salt concentration may be at saturation. The salt concentration maybe 3 M or lower and is typically from 0.1 to 2.5 M, from 0.3 to 1.9 M,from 0.5 to 1.8 M, from 0.7 to 1.7 M, from 0.9 to 1.6 M or from 1 M to1.4 M. The salt concentration is preferably from 150 mM to 1 M. Themethod is preferably carried out using a salt concentration of at least0.3 M, such as at least 0.4 M, at least 0.5 M, at least 0.6 M, at least0.8 M, at least 1.0 M, at least 1.5 M, at least 2.0 M, at least 2.5 M orat least 3.0 M. High salt concentrations provide a high signal to noiseratio and allow for currents indicative of the presence of a nucleotideto be identified against the background of normal current fluctuations.

The method is typically carried out in the presence of a buffer. In theexemplary apparatus discussed above, the buffer is present in theaqueous solution in the chamber. Any buffer may be used in the method ofthe invention. Typically, the buffer is phosphate buffer. Other suitablebuffers are HEPES and Tris-HCl buffer. The methods are typically carriedout at a pH of from 4.0 to 12.0, from 4.5 to 10.0, from 5.0 to 9.0, from5.5 to 8.8, from 6.0 to 8.7 or from 7.0 to 8.8 or 7.5 to 8.5. The pHused is preferably about 7.5.

The method may be carried out at from 0° C. to 100° C., from 15° C. to95° C., from 16° C. to 90° C., from 17° C. to 85° C., from 18° C. to 80°C., 19° C. to 70° C., or from 20° C. to 60° C. The methods are typicallycarried out at room temperature. The methods are optionally carried outat a temperature that supports enzyme function, such as about 37° C.

Polynucleotide Binding Protein

The strand characterisation method preferably comprises contacting thepolynucleotide with a polynucleotide binding protein such that theprotein controls the movement of the polynucleotide with respect to,such as through, the pore.

More preferably, the method comprises (a) contacting the polynucleotidewith a a pore of the invention and a polynucleotide binding protein suchthat the protein controls the movement of the polynucleotide withrespect to, such as through, the pore and (b) taking one or moremeasurements as the polynucleotide moves with respect to the pore,wherein the measurements are indicative of one or more characteristicsof the polynucleotide, and thereby characterising the polynucleotide.

More preferably, the method comprises (a) contacting the polynucleotidewith a a pore of the invention and a polynucleotide binding protein suchthat the protein controls the movement of the polynucleotide withrespect to, such as through, the pore and (b) measuring the currentthrough the pore as the polynucleotide moves with respect to the pore,wherein the current is indicative of one or more characteristics of thepolynucleotide, and thereby characterising the polynucleotide.

The polynucleotide binding protein may be any protein that is capable ofbinding to the polynucleotide and controlling its movement through thepore. It is straightforward in the art to determine whether or not aprotein binds to a polynucleotide. The protein typically interacts withand modifies at least one property of the polynucleotide. The proteinmay modify the polynucleotide by cleaving it to form individualnucleotides or shorter chains of nucleotides, such as di- ortrinucleotides. The protein may modify the polynucleotide by orientingit or moving it to a specific position, i.e. controlling its movement.

The polynucleotide binding protein is preferably derived from apolynucleotide handling enzyme. A polynucleotide handling enzyme is apolypeptide that is capable of interacting with and modifying at leastone property of a polynucleotide. The enzyme may modify thepolynucleotide by cleaving it to form individual nucleotides or shorterchains of nucleotides, such as di- or trinucleotides. The enzyme maymodify the polynucleotide by orienting it or moving it to a specificposition. The polynucleotide handling enzyme does not need to displayenzymatic activity as long as it is capable of binding thepolynucleotide and controlling its movement through the pore. Forinstance, the enzyme may be modified to remove its enzymatic activity ormay be used under conditions which prevent it from acting as an enzyme.Such conditions are discussed in more detail below.

The polynucleotide handling enzyme is preferably derived from anucleolytic enzyme. The polynucleotide handling enzyme used in theconstruct of the enzyme is more preferably derived from a member of anyof the Enzyme Classification (EC) groups 3.1.11, 3.1.13, 3.1.14, 3.1.15,3.1.16, 3.1.21, 3.1.22, 3.1.25, 3.1.26, 3.1.27, 3.1.30 and 3.1.31. Theenzyme may be any of those disclosed in International Application No.PCT/GB10/000133 (published as WO 2010/086603).

Preferred enzymes are polymerases, exonucleases, helicases andtopoisomerases, such as gyrases. Suitable enzymes include, but are notlimited to, exonuclease I from E. coli (SEQ ID NO: 11), exonuclease IIIenzyme from E. coli (SEQ ID NO: 13), RecJ from T. thermophilus (SEQ IDNO: 15) and bacteriophage lambda exonuclease (SEQ ID NO: 17), TatDexonuclease and variants thereof. Three subunits comprising the sequenceshown in SEQ ID NO: 15 or a variant thereof interact to form a trimerexonuclease. These exonucleases can also be used in the exonucleasemethod of the invention. The polymerase may be PyroPhage® 3173 DNAPolymerase (which is commercially available from Lucigen® Corporation),SD Polymerase (commercially available from Bioron®) or variants thereof.The enzyme is preferably Phi29 DNA polymerase (SEQ ID NO: 9) or avariant thereof. The topoisomerase is preferably a member of any of theMoiety Classification (EC) groups 5.99.1.2 and 5.99.1.3.

The enzyme is most preferably derived from a helicase, such as He1308Mbu (SEQ ID NO: 18), He1308 Csy (SEQ ID NO: 19), He1308 Tga (SEQ ID NO:20), He1308 Mhu (SEQ ID NO: 21), TraI Eco (SEQ ID NO: 22), XPD Mbu (SEQID NO: 23) or a variant thereof. Any helicase may be used in theinvention. The helicase may be or be derived from a He1308 helicase, aRecD helicase, such as TraI helicase or a TrwC helicase, a XPD helicaseor a Dda helicase. The helicase may be any of the helicases, modifiedhelicases or helicase constructs disclosed in International ApplicationNos. PCT/GB2012/052579 (published as WO 2013/057495); PCT/GB2012/053274(published as WO 2013/098562); PCT/GB2012/053273 (published asWO2013098561); PCT/GB2013/051925 (published as WO 2014/013260);PCT/GB2013/051924 (published as WO 2014/013259); PCT/GB2013/051928(published as WO 2014/013262) and PCT/GB2014/052736.

The helicase preferably comprises the sequence shown in SEQ ID NO: 25(Trwc Cba) or as variant thereof, the sequence shown in SEQ ID NO: 18(He1308 Mbu) or a variant thereof or the sequence shown in SEQ ID NO: 24(Dda) or a variant thereof. Variants may differ from the nativesequences in any of the ways discussed below for transmembrane pores. Apreferred variant of SEQ ID NO: 24 comprises (a) E94C and A360C or (b)E94C, A360C, C109A and C136A and then optionally (ΔM1)G1G2 (i.e.deletion of M1 and then addition G1 and G2).

Any number of helicases may be used in accordance with the invention.For instance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more helicases may beused. In some embodiments, different numbers of helicases may be used.

The method of the invention preferably comprises contacting thepolynucleotide with two or more helicases. The two or more helicases aretypically the same helicase. The two or more helicases may be differenthelicases.

The two or more helicases may be any combination of the helicasesmentioned above. The two or more helicases may be two or more Ddahelicases. The two or more helicases may be one or more Dda helicasesand one or more TrwC helicases. The two or more helicases may bedifferent variants of the same helicase.

The two or more helicases are preferably attached to one another. Thetwo or more helicases are more preferably covalently attached to oneanother. The helicases may be attached in any order and using anymethod. Preferred helicase constructs for use in the invention aredescribed in International Application Nos. PCT/GB2013/051925 (publishedas WO 2014/013260); PCT/GB2013/051924 (published as WO 2014/013259);PCT/GB2013/051928 (published as WO 2014/013262) and PCT/GB2014/052736.

A variant of SEQ ID NOs: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24or 25 is an enzyme that has an amino acid sequence which varies fromthat of SEQ ID NO: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25and which retains polynucleotide binding ability. This can be measuredusing any method known in the art. For instance, the variant can becontacted with a polynucleotide and its ability to bind to and movealong the polynucleotide can be measured. The variant may includemodifications that facilitate binding of the polynucleotide and/orfacilitate its activity at high salt concentrations and/or roomtemperature. Variants may be modified such that they bindpolynucleotides (i.e. retain polynucleotide binding ability) but do notfunction as a helicase (i.e. do not move along polynucleotides whenprovided with all the necessary components to facilitate movement, e.g.ATP and Mg²⁺). Such modifications are known in the art. For instance,modification of the Mg²⁺ binding domain in helicases typically resultsin variants which do not function as helicases. These types of variantsmay act as molecular brakes (see below).

Over the entire length of the amino acid sequence of SEQ ID NO: 9, 11,13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25, a variant will preferablybe at least 50% homologous to that sequence based on amino acididentity. More preferably, the variant polypeptide may be at least 55%,at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, atleast 85%, at least 90% and more preferably at least 95%, 97% or 99%homologous based on amino acid identity to the amino acid sequence ofSEQ ID NO: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25 over theentire sequence. There may be at least 80%, for example at least 85%,90% or 95%, amino acid identity over a stretch of 200 or more, forexample 230, 250, 270, 280, 300, 400, 500, 600, 700, 800, 900 or 1000 ormore, contiguous amino acids (“hard homology”). Homology is determinedas described above. The variant may differ from the wild-type sequencein any of the ways discussed above with reference to SEQ ID NO: 2 above.The enzyme may be covalently attached to the pore. Any method may beused to covalently attach the enzyme to the pore.

A preferred molecular brake is TrwC Cba-Q594A (SEQ ID NO: 25 with themutation Q594A). This variant does not function as a helicase (i.e.binds polynucleotides but does not move along them when provided withall the necessary components to facilitate movement, e.g. ATP and Mg²⁺).

In strand sequencing, the polynucleotide is translocated through thepore either with or against an applied potential. Exonucleases that actprogressively or processively on double stranded polynucleotides can beused on the cis side of the pore to feed the remaining single strandthrough under an applied potential or the trans side under a reversepotential. Likewise, a helicase that unwinds the double stranded DNA canalso be used in a similar manner. A polymerase may also be used. Thereare also possibilities for sequencing applications that require strandtranslocation against an applied potential, but the DNA must be first“caught” by the enzyme under a reverse or no potential. With thepotential then switched back following binding the strand will pass cisto trans through the pore and be held in an extended conformation by thecurrent flow. The single strand DNA exonucleases or single strand DNAdependent polymerases can act as molecular motors to pull the recentlytranslocated single strand back through the pore in a controlledstepwise manner, trans to cis, against the applied potential.

Any helicase may be used in the method. Helicases may work in two modeswith respect to the pore. First, the method is preferably carried outusing a helicase such that it moves the polynucleotide through the porewith the field resulting from the applied voltage. In this mode the 5′end of the polynucleotide is first captured in the pore, and thehelicase moves the polynucleotide into the pore such that it is passedthrough the pore with the field until it finally translocates through tothe trans side of the membrane. Alternatively, the method is preferablycarried out such that a helicase moves the polynucleotide through thepore against the field resulting from the applied voltage. In this modethe 3′ end of the polynucleotide is first captured in the pore, and thehelicase moves the polynucleotide through the pore such that it ispulled out of the pore against the applied field until finally ejectedback to the cis side of the membrane.

The method may also be carried out in the opposite direction. The 3′ endof the polynucleotide may be first captured in the pore and the helicasemay move the polynucleotide into the pore such that it is passed throughthe pore with the field until it finally translocates through to thetrans side of the membrane.

When the helicase is not provided with the necessary components tofacilitate movement or is modified to hinder or prevent its movement, itcan bind to the polynucleotide and act as a brake slowing the movementof the polynucleotide when it is pulled into the pore by the appliedfield. In the inactive mode, it does not matter whether thepolynucleotide is captured either 3′ or 5′ down, it is the applied fieldwhich pulls the polynucleotide into the pore towards the trans side withthe enzyme acting as a brake. When in the inactive mode, the movementcontrol of the polynucleotide by the helicase can be described in anumber of ways including ratcheting, sliding and braking. Helicasevariants which lack helicase activity can also be used in this way.

The polynucleotide may be contacted with the polynucleotide bindingprotein and the pore in any order. It is preferred that, when thepolynucleotide is contacted with the polynucleotide binding protein,such as a helicase, and the pore, the polynucleotide firstly forms acomplex with the protein. When the voltage is applied across the pore,the polynucleotide/protein complex then forms a complex with the poreand controls the movement of the polynucleotide through the pore.

Any steps in the method using a polynucleotide binding protein aretypically carried out in the presence of free nucleotides or freenucleotide analogues and an enzyme cofactor that facilitates the actionof the polynucleotide binding protein. The free nucleotides may be oneor more of any of the individual nucleotides discussed above. The freenucleotides include, but are not limited to, adenosine monophosphate(AMP), adenosine diphosphate (ADP), adenosine triphosphate (ATP),guanosine monophosphate (GMP), guanosine diphosphate (GDP), guanosinetriphosphate (GTP), thymidine monophosphate (TMP), thymidine diphosphate(TDP), thymidine triphosphate (TTP), uridine monophosphate (UMP),uridine diphosphate (UDP), uridine triphosphate (UTP), cytidinemonophosphate (CMP), cytidine diphosphate (CDP), cytidine triphosphate(CTP), cyclic adenosine monophosphate (cAMP), cyclic guanosinemonophosphate (cGMP), deoxyadenosine monophosphate (dAMP),deoxyadenosine diphosphate (dADP), deoxyadenosine triphosphate (dATP),deoxyguanosine monophosphate (dGMP), deoxyguanosine diphosphate (dGDP),deoxyguanosine triphosphate (dGTP), deoxythymidine monophosphate (dTMP),deoxythymidine diphosphate (dTDP), deoxythymidine triphosphate (dTTP),deoxyuridine monophosphate (dUMP), deoxyuridine diphosphate (dUDP),deoxyuridine triphosphate (dUTP), deoxycytidine monophosphate (dCMP),deoxycytidine diphosphate (dCDP) and deoxycytidine triphosphate (dCTP).The free nucleotides are preferably selected from AMP, TMP, GMP, CMP,UMP, dAMP, dTMP, dGMP or dCMP. The free nucleotides are preferablyadenosine triphosphate (ATP). The enzyme cofactor is a factor thatallows the construct to function. The enzyme cofactor is preferably adivalent metal cation. The divalent metal cation is preferably Mg²⁺,Mn²⁺, Ca²⁺ or Co²⁺. The enzyme cofactor is most preferably Mg²⁺.

Helicase(s) and Molecular Brake(s)

In a preferred embodiment, the method comprises:

-   -   (a) providing the polynucleotide with one or more helicases and        one or more molecular brakes attached to the polynucleotide;    -   (b) contacting the polynucleotide with a a pore of the invention        and applying a potential across the pore such that the one or        more helicases and the one or more molecular brakes are brought        together and both control the movement of the polynucleotide        with respect to, such as through, the pore;    -   (c) taking one or more measurements as the polynucleotide moves        with respect to the pore wherein the measurements are indicative        of one or more characteristics of the polynucleotide and thereby        characterising the polynucleotide.

This type of method is discussed in detail in the InternationalApplication PCT/GB2014/052737

The one or more helicases may be any of those discussed above. The oneor more molecular brakes may be any compound or molecule which binds tothe polynucleotide and slows the movement of the polynucleotide throughthe pore. The one or more molecular brakes preferably comprise one ormore compounds which bind to the polynucleotide. The one or morecompounds are preferably one or more macrocycles. Suitable macrocyclesinclude, but are not limited to, cyclodextrins, calixarenes, cyclicpeptides, crown ethers, cucurbiturils, pillararenes, derivatives thereofor a combination thereof. The cyclodextrin or derivative thereof may beany of those disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J.Am. Chem. Soc. 116, 6081-6088. The agent is more preferablyheptakis-6-amino-β-cyclodextrin (am₇-βCD),6-monodeoxy-6-monoamino-β-cyclodextrin (am₁-βCD) orheptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu₇-βCD).

The one or more molecular brakes are preferably one or more singlestranded binding proteins (SSB). The one or more molecular brakes aremore preferably a single-stranded binding protein (SSB) comprising acarboxy-terminal (C-terminal) region which does not have a net negativecharge or (ii) a modified SSB comprising one or more modifications inits C-terminal region which decreases the net negative charge of theC-terminal region. The one or more molecular brakes are most preferablyone of the SSBs disclosed in International Application No.PCT/GB2013/051924 (published as WO 2014/013259).

The one or more molecular brakes are preferably one or morepolynucleotide binding proteins. The polynucleotide binding protein maybe any protein that is capable of binding to the polynucleotide andcontrolling its movement through the pore. It is straightforward in theart to determine whether or not a protein binds to a polynucleotide. Theprotein typically interacts with and modifies at least one property ofthe polynucleotide. The protein may modify the polynucleotide bycleaving it to form individual nucleotides or shorter chains ofnucleotides, such as di- or trinucleotides. The moiety may modify thepolynucleotide by orienting it or moving it to a specific position, i.e.controlling its movement.

The polynucleotide binding protein is preferably derived from apolynucleotide handling enzyme. The one or more molecular brakes may bederived from any of the polynucleotide handling enzymes discussed above.Modified versions of Phi29 polymerase (SEQ ID NO: 8) which act asmolecular brakes are disclosed in U.S. Pat. No. 5,576,204. The one ormore molecular brakes are preferably derived from a helicase.

Any number of molecular brakes derived from a helicase may be used. Forinstance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more helicases may be used asmolecular brakes. If two or more helicases are be used as molecularbrakes, the two or more helicases are typically the same helicase. Thetwo or more helicases may be different helicases.

The two or more helicases may be any combination of the helicasesmentioned above. The two or more helicases may be two or more Ddahelicases. The two or more helicases may be one or more Dda helicasesand one or more TrwC helicases. The two or more helicases may bedifferent variants of the same helicase.

The two or more helicases are preferably attached to one another. Thetwo or more helicases are more preferably covalently attached to oneanother. The helicases may be attached in any order and using anymethod. The one or more molecular brakes derived from helicases arepreferably modified to reduce the size of an opening in thepolynucleotide binding domain through which in at least oneconformational state the polynucleotide can unbind from the helicase.This is disclosed in WO 2014/013260.

Preferred helicase constructs for use in the invention are described inInternational Application Nos. PCT/GB2013/051925 (published as WO2014/013260); PCT/GB2013/051924 (published as WO 2014/013259);PCT/GB2013/051928 (published as WO 2014/013262) and PCT/GB2014/052736.

If the one or more helicases are used in the active mode (i.e. when theone or more helicases are provided with all the necessary components tofacilitate movement, e.g. ATP and Mg²⁺), the one or more molecularbrakes are preferably (a) used in an inactive mode (i.e. are used in theabsence of the necessary components to facilitate movement or areincapable of active movement), (b) used in an active mode where the oneor more molecular brakes move in the opposite direction to the one ormore helicases or (c) used in an active mode where the one or moremolecular brakes move in the same direction as the one or more helicasesand more slowly than the one or more helicases.

If the one or more helicases are used in the inactive mode (i.e. whenthe one or more helicases are not provided with all the necessarycomponents to facilitate movement, e.g. ATP and Mg²⁺ or are incapable ofactive movement), the one or more molecular brakes are preferably (a)used in an inactive mode (i.e. are used in the absence of the necessarycomponents to facilitate movement or are incapable of active movement)or (b) used in an active mode where the one or more molecular brakesmove along the polynucleotide in the same direction as thepolynucleotide through the pore.

The one or more helicases and one or more molecular brakes may beattached to the polynucleotide at any positions so that they are broughttogether and both control the movement of the polynucleotide through thepore. The one or more helicases and one or more molecular brakes are atleast one nucleotide apart, such as at least 5, at least 10, at least50, at least 100, at least 500, at least 1000, at least 5000, at least10,000, at least 50,000 nucleotides or more apart. If the methodconcerns characterising a double stranded polynucleotide provided with aY adaptor at one end and a hairpin loop adaptor at the other end, theone or more helicases are preferably attached to the Y adaptor and theone or more molecular brakes are preferably attached to the hairpin loopadaptor. In this embodiment, the one or more molecular brakes arepreferably one or more helicases that are modified such that they bindthe polynucleotide but do not function as a helicase. The one or morehelicases attached to the Y adaptor are preferably stalled at a spaceras discussed in more detail below. The one or more molecular brakesattach to the hairpin loop adaptor are preferably not stalled at aspacer. The one or more helicases and the one or more molecular brakesare preferably brought together when the one or more helicases reach thehairpin loop. The one or more helicases may be attached to the Y adaptorbefore the Y adaptor is attached to the polynucleotide or after the Yadaptor is attached to the polynucleotide. The one or more molecularbrakes may be attached to the hairpin loop adaptor before the hairpinloop adaptor is attached to the polynucleotide or after the hairpin loopadaptor is attached to the polynucleotide.

The one or more helicases and the one or more molecular brakes arepreferably not attached to one another. The one or more helicases andthe one or more molecular brakes are more preferably not covalentlyattached to one another. The one or more helicases and the one or moremolecular brakes are preferably not attached as described inInternational Application Nos. PCT/GB2013/051925 (published as WO2014/013260); PCT/GB2013/051924 (published as WO 2014/013259);PCT/GB2013/051928 (published as WO 2014/013262) and PCT/GB2014/052736.

Spacers

The one or more helicases may be stalled at one or more spacers asdiscussed in International Application No. PCT/GB2014/050175. Anyconfiguration of one or more helicases and one or more spacers disclosedin the International Application may be used in this invention.

When a part of the polynucleotide enters the pore and moves through thepore along the field resulting from the applied potential, the one ormore helicases are moved past the spacer by the pore as thepolynucleotide moves through the pore. This is because thepolynucleotide (including the one or more spacers) moves through thepore and the one or more helicases remain on top of the pore.

The one or more spacers are preferably part of the polynucleotide, forinstance they interrupt(s) the polynucleotide sequence. The one or morespacers are preferably not part of one or more blocking molecules, suchas speed bumps, hybridised to the polynucleotide.

There may be any number of spacers in the polynucleotide, such as 1, 2,3, 4, 5, 6, 7, 8, 9, 10 or more spacers. There are preferably two, fouror six spacers in the polynucleotide. There may be one or more spacersin different regions of the polynucleotide, such as one or more spacersin the Y adaptor and/or hairpin loop adaptor.

The one or more spacers each provides an energy barrier which the one ormore helicases cannot overcome even in the active mode. The one or morespacers may stall the one or more helicases by reducing the traction ofthe helicase (for instance by removing the bases from the nucleotides inthe polynucleotide) or physically blocking movement of the one or morehelicases (for instance using a bulky chemical group).

The one or more spacers may comprise any molecule or combination ofmolecules that stalls the one or more helicases. The one or more spacersmay comprise any molecule or combination of molecules that prevents theone or more helicases from moving along the polynucleotide. It isstraightforward to determine whether or not the one or more helicasesare stalled at one or more spacers in the absence of a transmembranepore and an applied potential. For instance, the ability of a helicaseto move past a spacer and displace a complementary strand of DNA can bemeasured by PAGE.

The one or more spacers typically comprise a linear molecule, such as apolymer. The one or more spacers typically have a different structurefrom the polynucleotide. For instance, if the polynucleotide is DNA, theone or more spacers are typically not DNA. In particular, if thepolynucleotide is deoxyribonucleic acid (DNA) or ribonucleic acid (RNA),the one or more spacers preferably comprise peptide nucleic acid (PNA),glycerol nucleic acid (GNA), threose nucleic acid (TNA), locked nucleicacid (LNA) or a synthetic polymer with nucleotide side chains. The oneor more spacers may comprise one or more nucleotides in the oppositedirection from the polynucleotide. For instance, the one or more spacersmay comprise one or more nucleotides in the 3′ to 5′ direction when thepolynucleotide is in the 5′ to 3′ direction. The nucleotides may be anyof those discussed above.

The one or more spacers preferably comprises one or more nitroindoles,such as one or more 5-nitroindoles, one or more inosines, one or moreacridines, one or more 2-aminopurines, one or more 2-6-diaminopurines,one or more 5-bromo-deoxyuridines, one or more inverted thymidines(inverted dTs), one or more inverted dideoxy-thymidines (ddTs), one ormore dideoxy-cytidines (ddCs), one or more 5-methylcytidines, one ormore 5-hydroxymethylcytidines, one or more 2′-O-Methyl RNA bases, one ormore Iso-deoxycytidines (Iso-dCs), one or more Iso-deoxyguanosines(Iso-dGs), one or more iSpC3 groups (i.e. nucleotides which lack sugarand a base), one or more photo-cleavable (PC) groups, one or morehexandiol groups, one or more spacer 9 (iSp9) groups, one or more spacer18 (iSp18) groups, a polymer or one or more thiol connections. The oneor more spacers may comprise any combination of these groups. Many ofthese groups are commercially available from IDT® (Integrated DNATechnologies®).

The one or more spacers may contain any number of these groups. Forinstance, for 2-aminopurines, 2-6-diaminopurines, 5-bromo-deoxyuridines,inverted dTs, ddTs, ddCs, 5-methylcytidines, 5-hydroxymethylcytidines,2′-O-Methyl RNA bases, Iso-dCs, Iso-dGs, iSpC3 groups, PC groups,hexandiol groups and thiol connections, the one or more spacerspreferably comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more. The oneor more spacers preferably comprise 2, 3, 4, 5, 6, 7, 8 or more iSp9groups. The one or more spacers preferably comprise 2, 3, 4, 5 or 6 ormore iSp18 groups. The most preferred spacer is four iSp18 groups.

The polymer is preferably a polypeptide or a polyethylene glycol (PEG).The polypeptide preferably comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12or more amino acids. The PEG preferably comprises 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12 or more monomer units.

The one or more spacers preferably comprise one or more abasicnucleotides (i.e. nucleotides lacking a nucleobase), such as 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12 or more abasic nucleotides. The nucleobase can bereplaced by —H (idSp) or —OH in the abasic nucleotide. Abasic spacerscan be inserted into polynucleotides by removing the nucleobases fromone or more adjacent nucleotides. For instance, polynucleotides may bemodified to include 3-methyladenine, 7-methylguanine, 1,N6-ethenoadenineinosine or hypoxanthine and the nucleobases may be removed from thesenucleotides using Human Alkyladenine DNA Glycosylase (hAAG).Alternatively, polynucleotides may be modified to include uracil and thenucleobases removed with Uracil-DNA Glycosylase (UDG). In oneembodiment, the one or more spacers do not comprise any abasicnucleotides.

The one or more helicases may be stalled by (i.e. before) or on eachlinear molecule spacers. If linear molecule spacers are used, thepolynucleotide is preferably provided with a double stranded region ofpolynucleotide adjacent to the end of each spacer past which the one ormore helicases are to be moved. The double stranded region typicallyhelps to stall the one or more helicases on the adjacent spacer. Thepresence of the double stranded region(s) is particularly preferred ifthe method is carried out at a salt concentration of about 100 mM orlower. Each double stranded region is typically at least 10, such as atleast 12, nucleotides in length. If the polynucleotide used in theinvention is single stranded, a double stranded region may be formed byhybridising a shorter polynucleotide to a region adjacent to a spacer.The shorter polynucleotide is typically formed from the same nucleotidesas the polynucleotide, but may be formed from different nucleotides. Forinstance, the shorter polynucleotide may be formed from LNA.

If linear molecule spacers are used, the polynucleotide is preferablyprovided with a blocking molecule at the end of each spacer opposite tothe end past which the one or more helicases are to be moved. This canhelp to ensure that the one or more helicases remain stalled on eachspacer. It may also help retain the one or more helicases on thepolynucleotide in the case that it/they diffuse(s) off in solution. Theblocking molecule may be any of the chemical groups discussed belowwhich physically cause the one or more helicases to stall. The blockingmolecule may be a double stranded region of polynucleotide.

The one or more spacers preferably comprise one or more chemical groupswhich physically cause the one or more helicases to stall. The one ormore chemical groups are preferably one or more pendant chemical groups.The one or more chemical groups may be attached to one or morenucleobases in the polynucleotide. The one or more chemical groups maybe attached to the polynucleotide backbone. Any number of these chemicalgroups may be present, such as 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 ormore. Suitable groups include, but are not limited to, fluorophores,streptavidin and/or biotin, cholesterol, methylene blue, dinitrophenols(DNPs), digoxigenin and/or anti-digoxigenin and dibenzylcyclooctynegroups.

Different spacers in the polynucleotide may comprise different stallingmolecules. For instance, one spacer may comprise one of the linearmolecules discussed above and another spacer may comprise one or morechemical groups which physically cause the one or more helicases tostall. A spacer may comprise any of the linear molecules discussed aboveand one or more chemical groups which physically cause the one or morehelicases to stall, such as one or more abasics and a fluorophore.

Suitable spacers can be designed depending on the type of polynucleotideand the conditions under which the method of the invention is carriedout. Most helicases bind and move along DNA and so may be stalled usinganything that is not DNA. Suitable molecules are discussed above.

The method of the invention is preferably carried out in the presence offree nucleotides and/or the presence of a helicase cofactor. This isdiscussed in more detail below. In the absence of the transmembrane poreand an applied potential, the one or more spacers are preferably capableof stalling the one or more helicases in the presence of freenucleotides and/or the presence of a helicase cofactor.

If the method of the invention is carried out in the presence of freenucleotides and a helicase cofactor as discussed below (such that theone of more helicases are in the active mode), one or more longerspacers are typically used to ensure that the one or more helicases arestalled on the polynucleotide before they are contacted with thetransmembrane pore and a potential is applied. One or more shorterspacers may be used in the absence of free nucleotides and a helicasecofactor (such that the one or more helicases are in the inactive mode).

The salt concentration also affects the ability of the one or morespacers to stall the one or more helicases. In the absence of thetransmembrane pore and an applied potential, the one or more spacers arepreferably capable of stalling the one or more helicases at a saltconcentration of about 100 mM or lower. The higher the saltconcentration used in the method of the invention, the shorter the oneor more spacers that are typically used and vice versa.

Preferred combinations of features are shown in Table 4 below.

TABLE 4 Spacer length (i.e. Spacer number Free Helicase Polynucleotidecomposition* of *) Salt [ ] nucleotides? cofactor? DNA iSpC3 4 1 M YesYes DNA iSp18 4 100-1000 mM Yes Yes DNA iSp18 6 <100-1000 mM Yes Yes DNAiSp18 2 1 M Yes Yes DNA iSpC3 12 <100-1000 mM Yes Yes DNA iSpC3 20<100-1000 mM Yes Yes DNA iSp9 6 100-1000 mM Yes Yes DNA idSp 4 1 M YesYes

The method may concern moving two or more helicases past a spacer. Insuch instances, the length of the spacer is typically increased toprevent the trailing helicase from pushing the leading helicase past thespacer in the absence of the pore and applied potential. If the methodconcerns moving two or more helicases past one or more spacers, thespacer lengths discussed above may be increased at least 1.5 fold, such2 fold, 2.5 fold or 3 fold. For instance, if the method concerns movingtwo or more helicases past one or more spacers, the spacer lengths inthe third column of Table 4 above may be increased 1.5 fold, 2 fold, 2.5fold or 3 fold.

Membrane

The pore of the invention may be present in a membrane. In the methodsof the invention, the polynucleotide is typically contacted with thepore of the invention in a membrane. Any membrane may be used inaccordance with the invention. Suitable membranes are well-known in theart. The membrane is preferably an amphiphilic layer. An amphiphiliclayer is a layer formed from amphiphilic molecules, such asphospholipids, which have both hydrophilic and lipophilic properties.The amphiphilic molecules may be synthetic or naturally occurring.Non-naturally occurring amphiphiles and amphiphiles which form amonolayer are known in the art and include, for example, blockcopolymers (Gonzalez-Perez et al., Langmuir, 2009, 25, 10447-10450).Block copolymers are polymeric materials in which two or more monomersub-units that are polymerized together to create a single polymerchain. Block copolymers typically have properties that are contributedby each monomer sub-unit. However, a block copolymer may have uniqueproperties that polymers formed from the individual sub-units do notpossess. Block copolymers can be engineered such that one of the monomersub-units is hydrophobic (i.e. lipophilic), whilst the other sub-unit(s)are hydrophilic whilst in aqueous media. In this case, the blockcopolymer may possess amphiphilic properties and may form a structurethat mimics a biological membrane. The block copolymer may be a diblock(consisting of two monomer sub-units), but may also be constructed frommore than two monomer sub-units to form more complex arrangements thatbehave as amphipiles. The copolymer may be a triblock, tetrablock orpentablock copolymer. The membrane is preferably a triblock copolymermembrane.

Archaebacterial bipolar tetraether lipids are naturally occurring lipidsthat are constructed such that the lipid forms a monolayer membrane.These lipids are generally found in extremophiles that survive in harshbiological environments, thermophiles, halophiles and acidophiles. Theirstability is believed to derive from the fused nature of the finalbilayer. It is straightforward to construct block copolymer materialsthat mimic these biological entities by creating a triblock polymer thathas the general motif hydrophilic-hydrophobic-hydrophilic. This materialmay form monomeric membranes that behave similarly to lipid bilayers andencompass a range of phase behaviours from vesicles through to laminarmembranes. Membranes formed from these triblock copolymers hold severaladvantages over biological lipid membranes. Because the triblockcopolymer is synthesised, the exact construction can be carefullycontrolled to provide the correct chain lengths and properties requiredto form membranes and to interact with pores and other proteins.

Block copolymers may also be constructed from sub-units that are notclassed as lipid sub-materials; for example a hydrophobic polymer may bemade from siloxane or other non-hydrocarbon based monomers. Thehydrophilic sub-section of block copolymer can also possess low proteinbinding properties, which allows the creation of a membrane that ishighly resistant when exposed to raw biological samples. This head groupunit may also be derived from non-classical lipid head-groups.

Triblock copolymer membranes also have increased mechanical andenvironmental stability compared with biological lipid membranes, forexample a much higher operational temperature or pH range. The syntheticnature of the block copolymers provides a platform to customise polymerbased membranes for a wide range of applications.

The membrane is most preferably one of the membranes disclosed inInternational Application No. PCT/GB2013/052766 or PCT/GB2013/052767.

The amphiphilic molecules may be chemically-modified or functionalisedto facilitate coupling of the polynucleotide.

The amphiphilic layer may be a monolayer or a bilayer. The amphiphiliclayer is typically planar. The amphiphilic layer may be curved. Theamphiphilic layer may be supported.

Amphiphilic membranes are typically naturally mobile, essentially actingas two dimensional fluids with lipid diffusion rates of approximately10⁻⁸ cm s−1. This means that the pore and coupled polynucleotide cantypically move within an amphiphilic membrane.

The membrane may be a lipid bilayer. Lipid bilayers are models of cellmembranes and serve as excellent platforms for a range of experimentalstudies. For example, lipid bilayers can be used for in vitroinvestigation of membrane proteins by single-channel recording.Alternatively, lipid bilayers can be used as biosensors to detect thepresence of a range of substances. The lipid bilayer may be any lipidbilayer. Suitable lipid bilayers include, but are not limited to, aplanar lipid bilayer, a supported bilayer or a liposome. The lipidbilayer is preferably a planar lipid bilayer. Suitable lipid bilayersare disclosed in International Application No. PCT/GB08/000563(published as WO 2008/102121), International Application No.PCT/GB08/004127 (published as WO 2009/077734) and InternationalApplication No. PCT/GB2006/001057 (published as WO 2006/100484).

Methods for forming lipid bilayers are known in the art. Lipid bilayersare commonly formed by the method of Montal and Mueller (Proc. Natl.Acad. Sci. USA., 1972; 69: 3561-3566), in which a lipid monolayer iscarried on aqueous solution/air interface past either side of anaperture which is perpendicular to that interface. The lipid is normallyadded to the surface of an aqueous electrolyte solution by firstdissolving it in an organic solvent and then allowing a drop of thesolvent to evaporate on the surface of the aqueous solution on eitherside of the aperture. Once the organic solvent has evaporated, thesolution/air interfaces on either side of the aperture are physicallymoved up and down past the aperture until a bilayer is formed. Planarlipid bilayers may be formed across an aperture in a membrane or acrossan opening into a recess.

The method of Montal & Mueller is popular because it is a cost-effectiveand relatively straightforward method of forming good quality lipidbilayers that are suitable for protein pore insertion. Other commonmethods of bilayer formation include tip-dipping, painting bilayers andpatch-clamping of liposome bilayers.

Tip-dipping bilayer formation entails touching the aperture surface (forexample, a pipette tip) onto the surface of a test solution that iscarrying a monolayer of lipid. Again, the lipid monolayer is firstgenerated at the solution/air interface by allowing a drop of lipiddissolved in organic solvent to evaporate at the solution surface. Thebilayer is then formed by the Langmuir-Schaefer process and requiresmechanical automation to move the aperture relative to the solutionsurface.

For painted bilayers, a drop of lipid dissolved in organic solvent isapplied directly to the aperture, which is submerged in an aqueous testsolution. The lipid solution is spread thinly over the aperture using apaintbrush or an equivalent. Thinning of the solvent results information of a lipid bilayer. However, complete removal of the solventfrom the bilayer is difficult and consequently the bilayer formed bythis method is less stable and more prone to noise duringelectrochemical measurement.

Patch-clamping is commonly used in the study of biological cellmembranes. The cell membrane is clamped to the end of a pipette bysuction and a patch of the membrane becomes attached over the aperture.The method has been adapted for producing lipid bilayers by clampingliposomes which then burst to leave a lipid bilayer sealing over theaperture of the pipette. The method requires stable, giant andunilamellar liposomes and the fabrication of small apertures inmaterials having a glass surface.

Liposomes can be formed by sonication, extrusion or the Mozafari method(Colas et al. (2007) Micron 38:841-847).

In a preferred embodiment, the lipid bilayer is formed as described inInternational Application No. PCT/GB08/004127 (published as WO2009/077734). Advantageously in this method, the lipid bilayer is formedfrom dried lipids. In a most preferred embodiment, the lipid bilayer isformed across an opening as described in WO2009/077734(PCT/GB08/004127).

A lipid bilayer is formed from two opposing layers of lipids. The twolayers of lipids are arranged such that their hydrophobic tail groupsface towards each other to form a hydrophobic interior. The hydrophilichead groups of the lipids face outwards towards the aqueous environmenton each side of the bilayer. The bilayer may be present in a number oflipid phases including, but not limited to, the liquid disordered phase(fluid lamellar), liquid ordered phase, solid ordered phase (lamellargel phase, interdigitated gel phase) and planar bilayer crystals(lamellar sub-gel phase, lamellar crystalline phase).

Any lipid composition that forms a lipid bilayer may be used. The lipidcomposition is chosen such that a lipid bilayer having the requiredproperties, such surface charge, ability to support membrane proteins,packing density or mechanical properties, is formed. The lipidcomposition can comprise one or more different lipids. For instance, thelipid composition can contain up to 100 lipids. The lipid compositionpreferably contains 1 to 10 lipids. The lipid composition may comprisenaturally-occurring lipids and/or artificial lipids.

The lipids typically comprise a head group, an interfacial moiety andtwo hydrophobic tail groups which may be the same or different. Suitablehead groups include, but are not limited to, neutral head groups, suchas diacylglycerides (DG) and ceramides (CM); zwitterionic head groups,such as phosphatidylcholine (PC), phosphatidylethanolamine (PE) andsphingomyelin (SM); negatively charged head groups, such asphosphatidylglycerol (PG); phosphatidylserine (PS), phosphatidylinositol(PI), phosphatic acid (PA) and cardiolipin (CA); and positively chargedheadgroups, such as trimethylammonium-Propane (TAP). Suitableinterfacial moieties include, but are not limited to,naturally-occurring interfacial moieties, such as glycerol-based orceramide-based moieties. Suitable hydrophobic tail groups include, butare not limited to, saturated hydrocarbon chains, such as lauric acid(n-Dodecanolic acid), myristic acid (n-Tetradecononic acid), palmiticacid (n-Hexadecanoic acid), stearic acid (n-Octadecanoic) and arachidic(n-Eicosanoic); unsaturated hydrocarbon chains, such as oleic acid(cis-9-Octadecanoic); and branched hydrocarbon chains, such asphytanoyl. The length of the chain and the position and number of thedouble bonds in the unsaturated hydrocarbon chains can vary. The lengthof the chains and the position and number of the branches, such asmethyl groups, in the branched hydrocarbon chains can vary. Thehydrophobic tail groups can be linked to the interfacial moiety as anether or an ester. The lipids may be mycolic acid.

The lipids can also be chemically-modified. The head group or the tailgroup of the lipids may be chemically-modified. Suitable lipids whosehead groups have been chemically-modified include, but are not limitedto, PEG-modified lipids, such as1,2-Diacyl-sn-Glycero-3-Phosphoethanolamine-N-[Methoxy(Polyethyleneglycol)-2000]; functionalised PEG Lipids, such as1,2-Distearoyl-sn-Glycero-3 Phosphoethanolamine-N-[Biotinyl(PolyethyleneGlycol)2000]; and lipids modified for conjugation, such as1,2-Dioleoyl-sn-Glycero-3-Phosphoethanolamine-N-(succinyl) and1,2-Dipalmitoyl-sn-Glycero-3-Phosphoethanolamine-N-(Biotinyl). Suitablelipids whose tail groups have been chemically-modified include, but arenot limited to, polymerisable lipids, such as1,2-bis(10,12-tricosadiynoyl)-sn-Glycero-3-Phosphocholine; fluorinatedlipids, such as1-Palmitoyl-2-(16-Fluoropalmitoyl)-sn-Glycero-3-Phosphocholine;deuterated lipids, such as1,2-Dipalmitoyl-D62-sn-Glycero-3-Phosphocholine; and ether linkedlipids, such as 1,2-Di-O-phytanyl-sn-Glycero-3-Phosphocholine. Thelipids may be chemically-modified or functionalised to facilitatecoupling of the polynucleotide.

The amphiphilic layer, for example the lipid composition, typicallycomprises one or more additives that will affect the properties of thelayer. Suitable additives include, but are not limited to, fatty acids,such as palmitic acid, myristic acid and oleic acid; fatty alcohols,such as palmitic alcohol, myristic alcohol and oleic alcohol; sterols,such as cholesterol, ergosterol, lanosterol, sitosterol andstigmasterol; lysophospholipids, such as1-Acyl-2-Hydroxy-sn-Glycero-3-Phosphocholine; and ceramides.

In another preferred embodiment, the membrane comprises a solid statelayer. Solid state layers can be formed from both organic and inorganicmaterials including, but not limited to, microelectronic materials,insulating materials such as Si₃N₄, Al₂O₃, and SiO, organic andinorganic polymers such as polyamide, plastics such as Teflon® orelastomers such as two-component addition-cure silicone rubber, andglasses. The solid state layer may be formed from graphene. Suitablegraphene layers are disclosed in International Application No.PCT/US2008/010637 (published as WO 2009/035647). If the membranecomprises a solid state layer, the pore is typically present in anamphiphilic membrane or layer contained within the solid state layer,for instance within a hole, well, gap, channel, trench or slit withinthe solid state layer. The skilled person can prepare suitable solidstate/amphiphilic hybrid systems. Suitable systems are disclosed in WO2009/020682 and WO 2012/005857. Any of the amphiphilic membranes orlayers discussed above may be used.

The method is typically carried out using (i) an artificial amphiphiliclayer comprising a pore, (ii) an isolated, naturally-occurring lipidbilayer comprising a pore, or (iii) a cell having a pore insertedtherein. The method is typically carried out using an artificialamphiphilic layer, such as an artificial triblock copolymer layer. Thelayer may comprise other transmembrane and/or intramembrane proteins aswell as other molecules in addition to the pore. Suitable apparatus andconditions are discussed below. The method of the invention is typicallycarried out in vitro.

Coupling

The polynucleotide is preferably coupled to the membrane comprising thepore. The method may comprise coupling the polynucleotide to themembrane comprising the pore. The polynucleotide is preferably coupledto the membrane using one or more anchors. The polynucleotide may becoupled to the membrane using any known method.

Each anchor comprises a group which couples (or binds) to thepolynucleotide and a group which couples (or binds) to the membrane.Each anchor may covalently couple (or bind) to the polynucleotide and/orthe membrane. If a Y adaptor and/or a hairpin loop adaptors are used,the polynucleotide is preferably coupled to the membrane using theadaptor(s).

The polynucleotide may be coupled to the membrane using any number ofanchors, such as 2, 3, 4 or more anchors. For instance, a polynucleotidemay be coupled to the membrane using two anchors each of whichseparately couples (or binds) to both the polynucleotide and membrane.

The one or more anchors may comprise the one or more helicases and/orthe one or more molecular brakes.

If the membrane is an amphiphilic layer, such as a copolymer membrane ora lipid bilayer, the one or more anchors preferably comprise apolypeptide anchor present in the membrane and/or a hydrophobic anchorpresent in the membrane. The hydrophobic anchor is preferably a lipid,fatty acid, sterol, carbon nanotube, polypeptide, protein or amino acid,for example cholesterol, palmitate or tocopherol. In preferredembodiments, the one or more anchors are not the pore.

The components of the membrane, such as the amphiphilic molecules,copolymer or lipids, may be chemically-modified or functionalised toform the one or more anchors. Examples of suitable chemicalmodifications and suitable ways of functionalising the components of themembrane are discussed in more detail below. Any proportion of themembrane components may be functionalised, for example at least 0.01%,at least 0.1%, at least 1%, at least 10%, at least 25%, at least 50% or100%.

The polynucleotide may be coupled directly to the membrane. The one ormore anchors used to couple the polynucleotide to the membranepreferably comprise a linker. The one or more anchors may comprise oneor more, such as 2, 3, 4 or more, linkers. One linker may be used couplemore than one, such as 2, 3, 4 or more, polynucleotides to the membrane.

Preferred linkers include, but are not limited to, polymers, such aspolynucleotides, polyethylene glycols (PEGs), polysaccharides andpolypeptides. These linkers may be linear, branched or circular. Forinstance, the linker may be a circular polynucleotide. Thepolynucleotide may hybridise to a complementary sequence on the circularpolynucleotide linker.

The one or more anchors or one or more linkers may comprise a componentthat can be cut to broken down, such as a restriction site or aphotolabile group.

Functionalised linkers and the ways in which they can couple moleculesare known in the art. For instance, linkers functionalised withmaleimide groups will react with and attach to cysteine residues inproteins. In the context of this invention, the protein may be presentin the membrane or may be used to couple (or bind) to thepolynucleotide. This is discussed in more detail below.

Crosslinkage of polynucleotides can be avoided using a “lock and key”arrangement. Only one end of each linker may react together to form alonger linker and the other ends of the linker each react with thepolynucleotide or membrane respectively. Such linkers are described inInternational Application No. PCT/GB10/000132 (published as WO2010/086602).

The use of a linker is preferred in the sequencing embodiments discussedbelow. If a polynucleotide is permanently coupled directly to themembrane in the sense that it does not uncouple when interacting withthe pore (i.e. does not uncouple in step (b) or (e)), then some sequencedata will be lost as the sequencing run cannot continue to the end ofthe polynucleotide due to the distance between the membrane and thepore. If a linker is used, then the polynucleotide can be processed tocompletion.

The coupling may be permanent or stable. In other words, the couplingmay be such that the polynucleotide remains coupled to the membrane wheninteracting with the pore.

The coupling may be transient. In other words, the coupling may be suchthat the polynucleotide may decouple from the membrane when interactingwith the pore.

For certain applications, such as aptamer detection, the transientnature of the coupling is preferred. If a permanent or stable linker isattached directly to either the 5′ or 3′ end of a polynucleotide and thelinker is shorter than the distance between the membrane and thetransmembrane pore's channel, then some sequence data will be lost asthe sequencing run cannot continue to the end of the polynucleotide. Ifthe coupling is transient, then when the coupled end randomly becomesfree of the membrane, then the polynucleotide can be processed tocompletion. Chemical groups that form permanent/stable or transientlinks are discussed in more detail below. The polynucleotide may betransiently coupled to an amphiphilic layer or triblock copolymermembrane using cholesterol or a fatty acyl chain. Any fatty acyl chainhaving a length of from 6 to 30 carbon atom, such as hexadecanoic acid,may be used.

In preferred embodiments, a polynucleotide, such as a nucleic acid, iscoupled to an amphiphilic layer such as a triblock copolymer membrane orlipid bilayer. Coupling of nucleic acids to synthetic lipid bilayers hasbeen carried out previously with various different tethering strategies.These are summarised in Table 5 below.

TABLE 5 Anchor Type of comprising coupling Reference Thiol StableYoshina-Ishii, C. and S. G. Boxer (2003). “Arrays of mobile tetheredvesicles on supported lipid bilayers.” J Am Chem Soc 125(13): 3696-7.Biotin Stable Nikolov, V., R. Lipowsky, et al. (2007). “Behavior ofgiant vesicles with anchored DNA molecules.” Biophys J 92(12): 4356-68Cholesterol Transient Pfeiffer, I. and F. Hook (2004). “Bivalentcholesterol-based coupling of oligonucletides to lipid membraneassemblies.” J Am Chem Soc 126(33): 10224-5 Surfactant (e.g. Stable vanLengerich, B., R. J. Rawle, et al. Lipid, “Covalent attachment of lipidvesicles to a Palmitate, fluid-supported bilayer allows observation ofetc) DNA-mediated vesicle interactions.” Langmuir 26(11): 8666-72

Synthetic polynucleotides and/or linkers may be functionalised using amodified phosphoramidite in the synthesis reaction, which is easilycompatible for the direct addition of suitable anchoring groups, such ascholesterol, tocopherol, palmitate, thiol, lipid and biotin groups.These different attachment chemistries give a suite of options forattachment to polynucleotides. Each different modification group couplesthe polynucleotide in a slightly different way and coupling is notalways permanent so giving different dwell times for the polynucleotideto the membrane. The advantages of transient coupling are discussedabove.

Coupling of polynucleotides to a linker or to a functionalised membranecan also be achieved by a number of other means provided that acomplementary reactive group or an anchoring group can be added to thepolynucleotide. The addition of reactive groups to either end of apolynucleotide has been reported previously. A thiol group can be addedto the 5′ of ssDNA or dsDNA using T4 polynucleotide kinase and ATPγS(Grant, G. P. and P. Z. Qin (2007). “A facile method for attachingnitroxide spin labels at the 5′ terminus of nucleic acids.” NucleicAcids Res 35(10): e77). An azide group can be added to the 5′-phosphateof ssDNA or dsDNA using T4 polynucleotide kinase andγ-[2-Azidoethyl]-ATP or γ-[6-Azidohexyl]-ATP. Using thiol or Clickchemistry a tether, containing either a thiol, iodoacetamide OPSS ormaleimide group (reactive to thiols) or a DIBO (dibenzocyclooxtyne) oralkyne group (reactive to azides), can be covalently attached to thepolynucleotide. A more diverse selection of chemical groups, such asbiotin, thiols and fluorophores, can be added using terminal transferaseto incorporate modified oligonucleotides to the 3′ of ssDNA (Kumar, A.,P. Tchen, et al. (1988). “Nonradioactive labeling of syntheticoligonucleotide probes with terminal deoxynucleotidyl transferase.” AnalBiochem 169(2): 376-82). Streptavidin/biotin and/orstreptavidin/desthiobiotin coupling may be used for any otherpolynucleotide. The Examples below describes how a polynucleotide can becoupled to a membrane using streptavidin/biotin andstreptavidin/desthiobiotin. It may also be possible that anchors may bedirectly added to polynucleotides using terminal transferase withsuitably modified nucleotides (e.g. cholesterol or palmitate).

The one or more anchors preferably couple the polynucleotide to themembrane via hybridisation. Hybridisation in the one or more anchorsallows coupling in a transient manner as discussed above. Thehybridisation may be present in any part of the one or more anchors,such as between the one or more anchors and the polynucleotide, withinthe one or more anchors or between the one or more anchors and themembrane. For instance, a linker may comprise two or morepolynucleotides, such as 3, 4 or 5 polynucleotides, hybridised together.The one or more anchors may hybridise to the polynucleotide. The one ormore anchors may hybridise directly to the polynucleotide or directly toa Y adaptor and/or leader sequence attached to the polynucleotide ordirectly to a hairpin loop adaptor attached to the polynucleotide (asdiscussed below). Alternatively, the one or more anchors may behybridised to one or more, such as 2 or 3, intermediate polynucleotides(or “splints”) which are hybridised to the polynucleotide, to a Yadaptor and/or leader sequence attached to the polynucleotide or to ahairpin loop adaptor attached to the polynucleotide (as discussedbelow).

The one or more anchors may comprise a single stranded or doublestranded polynucleotide. One part of the anchor may be ligated to asingle stranded or double stranded polynucleotide. Ligation of shortpieces of ssDNA have been reported using T4 RNA ligase I (Troutt, A. B.,M. G. McHeyzer-Williams, et al. (1992). “Ligation-anchored PCR: a simpleamplification technique with single-sided specificity.” Proc Natl AcadSci USA 89(20): 9823-5). Alternatively, either a single stranded ordouble stranded polynucleotide can be ligated to a double strandedpolynucleotide and then the two strands separated by thermal or chemicaldenaturation. To a double stranded polynucleotide, it is possible to addeither a piece of single stranded polynucleotide to one or both of theends of the duplex, or a double stranded polynucleotide to one or bothends. For addition of single stranded polynucleotides to the a doublestranded polynucleotide, this can be achieved using T4 RNA ligase I asfor ligation to other regions of single stranded polynucleotides. Foraddition of double stranded polynucleotides to a double strandedpolynucleotide then ligation can be “blunt-ended”, with complementary 3′dA/dT tails on the polynucleotide and added polynucleotide respectively(as is routinely done for many sample prep applications to preventconcatemer or dimer formation) or using “sticky-ends” generated byrestriction digestion of the polynucleotide and ligation of compatibleadapters. Then, when the duplex is melted, each single strand will haveeither a 5′ or 3′ modification if a single stranded polynucleotide wasused for ligation or a modification at the 5′ end, the 3′ end or both ifa double stranded polynucleotide was used for ligation.

If the polynucleotide is a synthetic strand, the one or more anchors canbe incorporated during the chemical synthesis of the polynucleotide. Forinstance, the polynucleotide can be synthesised using a primer having areactive group attached to it.

Adenylated polynucleotides are intermediates in ligation reactions,where an adenosine-monophosphate is attached to the 5′-phosphate of thepolynucleotide. Various kits are available for generation of thisintermediate, such as the 5′ DNA Adenylation Kit from NEB. Bysubstituting ATP in the reaction for a modified nucleotide triphosphate,then addition of reactive groups (such as thiols, amines, biotin,azides, etc) to the 5′ of a polynucleotide can be possible. It may alsobe possible that anchors could be directly added to polynucleotidesusing a 5′ DNA adenylation kit with suitably modified nucleotides (e.g.cholesterol or palmitate).

A common technique for the amplification of sections of genomic DNA isusing polymerase chain reaction (PCR). Here, using two syntheticoligonucleotide primers, a number of copies of the same section of DNAcan be generated, where for each copy the 5′ of each strand in theduplex will be a synthetic polynucleotide. Single or multiplenucleotides can be added to 3′ end of single or double stranded DNA byemploying a polymerase. Examples of polymerases which could be usedinclude, but are not limited to, Terminal Transferase, Klenow and E.coli Poly(A) polymerase). By substituting ATP in the reaction for amodified nucleotide triphosphate then anchors, such as a cholesterol,thiol, amine, azide, biotin or lipid, can be incorporated into doublestranded polynucleotides. Therefore, each copy of the amplifiedpolynucleotide will contain an anchor.

Ideally, the polynucleotide is coupled to the membrane without having tofunctionalise the polynucleotide. This can be achieved by coupling theone or more anchors, such as a polynucleotide binding protein or achemical group, to the membrane and allowing the one or more anchors tointeract with the polynucleotide or by functionalising the membrane. Theone or more anchors may be coupled to the membrane by any of the methodsdescribed herein. In particular, the one or more anchors may compriseone or more linkers, such as maleimide functionalised linkers.

In this embodiment, the polynucleotide is typically RNA, DNA, PNA, TNAor LNA and may be double or single stranded. This embodiment isparticularly suited to genomic DNA polynucleotides.

The one or more anchors can comprise any group that couples to, binds toor interacts with single or double stranded polynucleotides, specificnucleotide sequences within the polynucleotide or patterns of modifiednucleotides within the polynucleotide, or any other ligand that ispresent on the polynucleotide.

Suitable binding proteins for use in anchors include, but are notlimited to, E. coli single stranded binding protein, P5 single strandedbinding protein, T4 gp32 single stranded binding protein, the TOPO VdsDNA binding region, human histone proteins, E. coli HU DNA bindingprotein and other archaeal, prokaryotic or eukaryotic single stranded ordouble stranded polynucleotide (or nucleic acid) binding proteins,including those listed below.

The specific nucleotide sequences could be sequences recognised bytranscription factors, ribosomes, endonucleases, topoisomerases orreplication initiation factors. The patterns of modified nucleotidescould be patterns of methylation or damage.

The one or more anchors can comprise any group which couples to, bindsto, intercalates with or interacts with a polynucleotide. The group mayintercalate or interact with the polynucleotide via electrostatic,hydrogen bonding or Van der Waals interactions. Such groups include alysine monomer, poly-lysine (which will interact with ssDNA or dsDNA),ethidium bromide (which will intercalate with dsDNA), universal bases oruniversal nucleotides (which can hybridise with any polynucleotide) andosmium complexes (which can react to methylated bases). A polynucleotidemay therefore be coupled to the membrane using one or more universalnucleotides attached to the membrane. Each universal nucleotide may becoupled to the membrane using one or more linkers. The universalnucleotide preferably comprises one of the following nucleobases:hypoxanthine, 4-nitroindole, 5-nitroindole, 6-nitroindole, formylindole,3-nitropyrrole, nitroimidazole, 4-nitropyrazole, 4-nitrobenzimidazole,5-nitroindazole, 4-aminobenzimidazole or phenyl (C6-aromatic ring). Theuniversal nucleotide more preferably comprises one of the followingnucleosides: 2′-deoxyinosine, inosine, 7-deaza-2′-deoxyinosine,7-deaza-inosine, 2-aza-deoxyinosine, 2-aza-inosine, 2-0′-methylinosine,4-nitroindole 2′-deoxyribonucleoside, 4-nitroindole ribonucleoside,5-nitroindole 2′-deoxyribonucleoside, 5-nitroindole ribonucleoside,6-nitroindole 2′-deoxyribonucleoside, 6-nitroindole ribonucleoside,3-nitropyrrole 2′-deoxyribonucleoside, 3-nitropyrrole ribonucleoside, anacyclic sugar analogue of hypoxanthine, nitroimidazole2′-deoxyribonucleoside, nitroimidazole ribonucleoside, 4-nitropyrazole2′-deoxyribonucleoside, 4-nitropyrazole ribonucleoside,4-nitrobenzimidazole 2′-deoxyribonucleoside, 4-nitrobenzimidazoleribonucleoside, 5-nitroindazole 2′-deoxyribonucleoside, 5-nitroindazoleribonucleoside, 4-aminobenzimidazole 2′-deoxyribonucleoside,4-aminobenzimidazole ribonucleoside, phenyl C-ribonucleoside, phenylC-2′-deoxyribosyl nucleoside, 2′-deoxynebularine, 2′-deoxyisoguanosine,K-2′-deoxyribose, P-2′-deoxyribose and pyrrolidine. The universalnucleotide more preferably comprises 2′-deoxyinosine. The universalnucleotide is more preferably IMP or dIMP. The universal nucleotide ismost preferably dPMP (2′-Deoxy-P-nucleoside monophosphate) or dKMP(N6-methoxy-2, 6-diaminopurine monophosphate).

The one or more anchors may couple to (or bind to) the polynucleotidevia Hoogsteen hydrogen bonds (where two nucleobases are held together byhydrogen bonds) or reversed Hoogsteen hydrogen bonds (where onenucleobase is rotated through 180° with respect to the othernucleobase). For instance, the one or more anchors may comprise one ormore nucleotides, one or more oligonucleotides or one or morepolynucleotides which form Hoogsteen hydrogen bonds or reversedHoogsteen hydrogen bonds with the polynucleotide. These types ofhydrogen bonds allow a third polynucleotide strand to wind around adouble stranded helix and form a triplex. The one or more anchors maycouple to (or bind to) a double stranded polynucleotide by forming atriplex with the double stranded duplex.

In this embodiment at least 1%, at least 10%, at least 25%, at least 50%or 100% of the membrane components may be functionalised.

Where the one or more anchors comprise a protein, they may be able toanchor directly into the membrane without further functonalisation, forexample if it already has an external hydrophobic region which iscompatible with the membrane. Examples of such proteins include, but arenot limited to, transmembrane proteins, intramembrane proteins andmembrane proteins. Alternatively the protein may be expressed with agenetically fused hydrophobic region which is compatible with themembrane. Such hydrophobic protein regions are known in the art.

The one or more anchors are preferably mixed with the polynucleotidebefore contacting with the membrane, but the one or more anchors may becontacted with the membrane and subsequently contacted with thepolynucleotide.

In another aspect the polynucleotide may be functionalised, usingmethods described above, so that it can be recognised by a specificbinding group. Specifically the polynucleotide may be functionalisedwith a ligand such as biotin (for binding to streptavidin), amylose (forbinding to maltose binding protein or a fusion protein), Ni-NTA (forbinding to poly-histidine or poly-histidine tagged proteins) or apeptides (such as an antigen).

According to a preferred embodiment, the one or more anchors may be usedto couple a polynucleotide to the membrane when the polynucleotide isattached to a leader sequence which preferentially threads into thepore. Leader sequences are discussed in more detail below. Preferably,the polynucleotide is attached (such as ligated) to a leader sequencewhich preferentially threads into the pore. Such a leader sequence maycomprise a homopolymeric polynucleotide or an abasic region. The leadersequence is typically designed to hybridise to the one or more anchorseither directly or via one or more intermediate polynucleotides (orsplints). In such instances, the one or more anchors typically comprisea polynucleotide sequence which is complementary to a sequence in theleader sequence or a sequence in the one or more intermediatepolynucleotides (or splints). In such instances, the one or more splintstypically comprise a polynucleotide sequence which is complementary to asequence in the leader sequence.

An example of a molecule used in chemical attachment is EDC(1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride). Reactivegroups can also be added to the 5′ of polynucleotides using commerciallyavailable kits (Thermo Pierce, Part No. 22980). Suitable methodsinclude, but are not limited to, transient affinity attachment usinghistidine residues and Ni-NTA, as well as more robust covalentattachment by reactive cysteines, lysines or non natural amino acids.

Double Stranded Polynucleotide

The polynucleotide may be double stranded. If the polynucleotide isdouble stranded, the method preferably further comprises before thecontacting step ligating a bridging moiety, such as a hairpin loop, toone end of the polynucleotide. The two strands of the polynucleotide maythen be separated as or before the polynucleotide is contacted with thepore in accordance with the invention. The two strands may be separatedas the polynucleotide movement through the pore is controlled by apolynucleotide binding protein, such as a helicase, or molecular brake.

Linking and interrogating both strands on a double stranded construct inthis way increases the efficiency and accuracy of characterisation.

The bridging moiety is capable of linking the two strands of the targetpolynucleotide. The bridging moiety typically covalently links the twostrands of the target polynucleotide. The bridging moiety can beanything that is capable of linking the two strands of the targetpolynucleotide, provided that the bridging moiety does not interferewith movement of the single stranded polynucleotide through thetransmembrane pore.

The bridging moiety may be linked to the target polynucleotide by anysuitable means known in the art. The bridging moiety may be synthesisedseparately and chemically attached or enzymatically ligated to thetarget polynucleotide. Alternatively, the bridging moiety may begenerated in the processing of the target polynucleotide.

The bridging moiety is linked to the target polynucleotide at or nearone end of the target polynucleotide. The bridging moiety is preferablylinked to the target polynucleotide within 10 nucleotides of the end ofthe target polynucleotide

Suitable bridging moieties include, but are not limited to a polymericlinker, a chemical linker, a polynucleotide or a polypeptide.Preferably, the bridging moiety comprises DNA, RNA, modified DNA (suchas abasic DNA), RNA, PNA, LNA or PEG. The bridging moiety is morepreferably DNA or RNA.

The bridging moiety is most preferably a hairpin loop or a hairpin loopadaptor. Suitable hairpin adaptors can be designed using methods knownin the art. The hairpin loop may be any length. The hairpin loop istypically 110 or fewer nucleotides, such as 100 or fewer nucleotides, 90or fewer nucleotides, 80 or fewer nucleotides, 70 or fewer nucleotides,60 or fewer nucleotides, 50 or fewer nucleotides, 40 or fewernucleotides, 30 or fewer nucleotides, 20 or fewer nucleotides or 10 orfewer nucleotides, in length. The hairpin loop is preferably from about1 to 110, from 2 to 100, from 5 to 80 or from 6 to 50 nucleotides inlength. Longer lengths of the hairpin loop, such as from 50 to 110nucleotides, are preferred if the loop is involved in the differentialselectability of the adaptor. Similarly, shorter lengths of the hairpinloop, such as from 1 to 5 nucleotides, are preferred if the loop is notinvolved in the selectable binding as discussed below.

The hairpin adaptor may be ligated to either end of the first and/orsecond polynucleotide, i.e. the 5′ or the 3′ end. The hairpin adaptormay be ligated to the first and/or second polynucleotide using anymethod known in the art. The hairpin adaptor may be ligated using aligase, such as T4 DNA ligase, E. coli DNA ligase, Taq DNA ligase, TmaDNA ligase and 9° N DNA ligase.

The two strands of the polynucleotide may be separated using any methodknown in the art. For instance, they may be separated by apolynucleotide binding protein or using conditions which favourdehybridisation (examples of conditions which favour dehybridisationinclude, but are not limited to, high temperature, high pH and theaddition of agents that can disrupt hydrogen bonding or base pairing,such as formamide and urea).

The hairpin adaptor preferably comprises a selectable binding moiety.This allows the first and/or second polynucleotide to be purified orisolated. A selectable binding moiety is a moiety that can be selectedon the basis of its binding properties. Hence, a selectable bindingmoiety is preferably a moiety that specifically binds to a surface. Aselectable binding moiety specifically binds to a surface if it binds tothe surface to a much greater degree than any other moiety used in theinvention. In preferred embodiments, the moiety binds to a surface towhich no other moiety used in the invention binds.

Suitable selective binding moieties are known in the art. Preferredselective binding moieties include, but are not limited to, biotin, apolynucleotide sequence, antibodies, antibody fragments, such as Fab andScSv, antigens, polynucleotide binding proteins, poly histidine tailsand GST tags. The most preferred selective binding moieties are biotinand a selectable polynucleotide sequence. Biotin specifically binds to asurface coated with avidins. Selectable polynucleotide sequencesspecifically bind (i.e. hybridise) to a surface coated with homologussequences. Alternatively, selectable polynucleotide sequencesspecifically bind to a surface coated with polynucleotide bindingproteins.

The hairpin adaptor and/or the selectable binding moiety may comprise aregion that can be cut, nicked, cleaved or hydrolysed. Such a region canbe designed to allow the first and/or second polynucleotide to beremoved from the surface to which it is bound following purification orisolation. Suitable regions are known in the art. Suitable regionsinclude, but are not limited to, an RNA region, a region comprisingdesthiobiotin and streptavidin, a disulphide bond and a photocleavableregion.

The double stranded target polynucleotide preferably comprises a leadersequence at the opposite end of the bridging moiety, such as a hairpinloop or hairpin loop adaptor. Leader sequences are discussed in moredetail below.

Round the Corner Sequencing

In a preferred embodiment, a target double stranded polynucleotide isprovided with a bridging moiety, such as a hairpin loop or hairpin loopadaptor, at one end and the method comprises contacting thepolynucleotide with the pore such that both strands of thepolynucleotide move through the pore and taking one or more measurementsas the both strands of the polynucleotide move with respect to the porewherein the measurements are indicative of one or more characteristicsof the strands of the polynucleotide and thereby characterising thetarget double stranded polynucleotide. In another preferred embodiment,a target double stranded polynucleotide is provided with a bridgingmoiety, such as a hairpin loop or hairpin loop adaptor, at one end andthe method comprises contacting the polynucleotide with the pore andexonuclease such that both strands of the polynucleotide are digested toform individual nucleotides. Any of the embodiments discussed aboveequally apply to this embodiment.

Leader Sequence

Before the contacting step in the strand characterisation/sequencingmethod, the method preferably comprises attaching to the polynucleotidea leader sequence which preferentially threads into the pore. The leadersequence facilitates the method of the invention. The leader sequence isdesigned to preferentially thread into the pore and thereby facilitatethe movement of polynucleotide through the pore. The leader sequence canalso be used to link the polynucleotide to the one or more anchors asdiscussed above.

The leader sequence typically comprises a polymer. The polymer ispreferably negatively charged. The polymer is preferably apolynucleotide, such as DNA or RNA, a modified polynucleotide (such asabasic DNA), PNA, LNA, polyethylene glycol (PEG) or a polypeptide. Theleader preferably comprises a polynucleotide and more preferablycomprises a single stranded polynucleotide. The leader sequence cancomprise any of the polynucleotides discussed above. The single strandedleader sequence most preferably comprises a single strand of DNA, suchas a poly dT section. The leader sequence preferably comprises the oneor more spacers.

The leader sequence can be any length, but is typically 10 to 150nucleotides in length, such as from 20 to 150 nucleotides in length. Thelength of the leader typically depends on the transmembrane pore used inthe method.

The leader sequence is preferably part of a Y adaptor as defined below.

Double Coupling

The method of the invention may involve double coupling of a doublestranded polynucleotide. In a preferred embodiment, the method of theinvention comprises:

(a) providing the double stranded polynucleotide with a Y adaptor at oneend and a bridging moiety adaptor, such as a hairpin loop adaptor, atthe other end, wherein the Y adaptor comprises one or more first anchorsfor coupling the polynucleotide to the membrane, wherein the bridgingmoiety adaptor comprises one or more second anchors for coupling thepolynucleotide to the membrane and wherein the strength of coupling ofthe bridging moiety adaptor to the membrane is greater than the strengthof coupling of the Y adaptor to the membrane;

(b) contacting the polynucleotide provided in step (a) with a pore theinvention such that the polynucleotide moves with respect to, such asthrough, the pore; and

(c) taking one or more measurements as the polynucleotide moves withrespect to the pore, wherein the measurements are indicative of one ormore characteristics of the polynucleotide, and thereby characterisingthe target polynucleotide.

This type of method is discussed in detail in the UK Application No.1406147.7.

The double stranded polynucleotide is provided with a Y adaptor at oneend and a bridging moiety adaptor at the other end. The Y adaptor and/orthe bridging moiety adaptor are typically polynucleotide adaptors. Theymay be formed from any of the polynucleotides discussed above.

The Y adaptor typically comprises (a) a double stranded region and (b) asingle stranded region or a region that is not complementary at theother end. The Y adaptor may be described as having an overhang if itcomprises a single stranded region. The presence of a non-complementaryregion in the Y adaptor gives the adaptor its Y shape since the twostrands typically do not hybridise to each other unlike the doublestranded portion. The Y adaptor comprises the one or more first anchors.Anchors are discussed in more detail above.

The Y adaptor preferably comprises a leader sequence whichpreferentially threads into the pore. This is discussed above.

The bridging moiety adaptor preferably comprises a selectable bindingmoiety as discussed above. The bridging moiety adaptor and/or theselectable binding moiety may comprise a region that can be cut, nicked,cleaved or hydrolysed as discussed above.

If one or more helicases and one or more molecular brakes are used asdiscussed above, the Y adaptor preferably comprises the one or morehelicases and the bridging moiety adaptor preferably comprises the oneor more molecular brakes.

The Y adaptor and/or the bridging moiety adaptor may be ligated to thepolynucleotide using any method known in the art. One or both of theadaptors may be ligated using a ligase, such as T4 DNA ligase, E. coliDNA ligase, Taq DNA ligase, Tma DNA ligase and 9° N DNA ligase.Alternatively, the adaptors may be added to the polynucleotide using themethods of the invention discussed below.

In a preferred embodiment, step a) of the method comprises modifying thedouble stranded polynucleotide so that it comprises the Y adaptor at oneend and the bridging moiety adaptor at the other end. Any manner ofmodification can be used. The method preferably comprises modifying thedouble stranded polynucleotide in accordance with the invention. This isdiscussed in more detail below. The methods of modification andcharacterisation may be combined in any way.

The strength of coupling (or binding) of the bridging moiety adaptor tothe membrane is greater than the strength of coupling (or binding) ofthe Y adaptor to the membrane. This can be measured in any way. Asuitable method for measuring the strength of coupling (or binding) isdisclosed in the Examples of the UK Application No. 1406147.7.

The strength of coupling (or binding) of the bridging moiety adaptor ispreferably at least 1.5 times the strength of coupling (or binding) ofthe Y adaptor, such as at least twice, at least three times, at leastfour times, at least five or at least ten times the strength of coupling(or binding) of the anchor adaptor. The affinity constant (Kd) of thebridging moiety adaptor for the membrane is preferably at least 1.5times the affinity constant of the Y adaptor, such as at least twice, atleast three times, at least four times, at least five or at least tentimes the strength of coupling of the Y adaptor.

There are several ways in which the bridging moiety adaptor couples (orbinds) more strongly to the membrane than the Y adaptor. For instance,the bridging moiety adaptor may comprise more anchors than the Yadaptor. For instance, the bridging moiety adaptor may comprise 2, 3 ormore second anchors whereas the Y adaptor may comprise one first anchor.

The strength of coupling (or binding) of the one or more second anchorsto the membrane may be greater than the strength of coupling (orbinding) of the one or more first anchors to the membrane. The strengthof coupling (or binding) of the one or more second anchors to thebridging moiety adaptor may be greater than the strength of coupling (orbinding) of the one or more first anchors to the Y adaptor. The one ormore first anchors and the one or more second anchors may be attached totheir respective adaptors via hybridisation and the strength ofhybridisation is greater in the one or more second anchors than in theone or more first anchors. Any combination of these embodiments may alsobe used in the invention. Strength of coupling (or binding) may bemeasure using known techniques in the art.

The one or more second anchors preferably comprise one or more groupswhich couple(s) (or bind(s)) to the membrane with a greater strengththan the one or more groups in the one or more first anchors whichcouple(s) (or bind(s)) to the membrane. In preferred embodiments, thebridging moiety adaptor/one or more second anchors couple (or bind) tothe membrane using cholesterol and the Y adaptor/one or more firstanchors couple (or bind) to the membrane using palmitate. Cholesterolbinds to triblock copolymer membranes and lipid membranes more stronglythan palmitate. In an alternative embodiment, the bridging moietyadaptor/one or more second anchors couple (or bind) to the membraneusing a mono-acyl species, such as palmitate, and the Y adaptor/one ormore first anchors couple (or bind) to the membrane using a diacylspecies, such as dipalmitoylphosphatidylcholine.

Adding Hairpin Loops and Leader Sequences

Before provision, a double stranded polynucleotide may be contacted witha MuA transposase and a population of double stranded MuA substrates,wherein a proportion of the substrates in the population are Y adaptorscomprising the leader sequence and wherein a proportion of thesubstrates in the population are hairpin loop adaptors. The transposasefragments the double stranded polynucleotide analyte and ligates MuAsubstrates to one or both ends of the fragments. This produces aplurality of modified double stranded polynucleotides comprising theleader sequence at one end and the hairpin loop at the other. Themodified double stranded polynucleotides may then be investigated usingthe method of the invention.

Each substrate in the population preferably comprises at least oneoverhang of universal nucleotides such that the transposase fragmentsthe template polynucleotide and ligates a substrate to one or both endsof the double stranded fragments and thereby produces a plurality offragment/substrate constructs and wherein the method further comprisesligating the overhangs to the fragments in the constructs and therebyproducing a plurality of modified double stranded polynucleotides.Suitable universal nucleotides are discussed above. The overhang ispreferably five nucleotides in length.

Alternatively, each substrate in population preferably comprises (i) atleast one overhang and (ii) at least one nucleotide in the same strandas the at least one overhang which comprises a nucleoside that is notpresent in the template polynucleotide such that the transposasefragments the template polynucleotide and ligates a substrate to one orboth ends of the double stranded fragments and thereby produces aplurality of fragment/substrate constructs, and wherein the methodfurther comprises (a) removing the overhangs from the constructs byselectively removing the at least one nucleotide and thereby producing aplurality of double stranded constructs comprising single stranded gapsand (b) repairing the single stranded gaps in the constructs and therebyproducing a plurality of modified double stranded polynucleotides. Thepolynucleotide typically comprises the nucleosides deoxyadenosine (dA),deoxyuridine (dU) and/or thymidine (dT), deoxyguanosine (dG) anddeoxycytidine (dC). The nucleoside that is not present in thepolynucleotide is preferably abasic, adenosine (A), uridine (U),5-methyluridine (m⁵U), cytidine (C) or guanosine (G) or comprises urea,5, 6 dihydroxythymine, thymine glycol, 5-hydroxy-5 methylhydanton,uracil glycol, 6-hydroxy-5, 6-dihdrothimine, methyltartronylurea, 7,8-dihydro-8-oxoguanine (8-oxoguanine), 8-oxoadenine, fapy-guanine,methy-fapy-guanine, fapy-adenine, aflatoxin B1-fapy-guanine,5-hydroxy-cytosine, 5-hydroxy-uracil, 3-methyladenine, 7-methylguanine,1,N6-ethenoadenine, hypoxanthine, 5-hydroxyuracil,5-hydroxymethyluracil, 5-formyluracil or a cis-syn-cyclobutanepyrimidine dimer. The at least one nucleotide preferably is 10nucleotides or fewer from the overhang. The at least one nucleotide isthe first nucleotide in the overhang. All of the nucleotides in theoverhang preferably comprise a nucleoside that is not present in thetemplate polynucleotide.

These MuA based methods are disclosed in International Application No.PCT/GB2014/052505. They are also discussed in detail in the UKApplication No. 1406147.7.

One or more helicases may be attached to the MuA substrate Y adaptorsbefore they are contacted with the double stranded polynucleotide andMuA transposase. Alternatively, one or more helicases may be attached tothe MuA substrate Y adaptors before they are contacted with the doublestranded polynucleotide and MuA transposase.

One or more molecular brakes may be attached to the MuA substratehairpin loop adaptors before they are contacted with the double strandedpolynucleotide and MuA transposase. Alternatively, one or more molecularbrakes may be attached to the MuA substrate hairpin loop adaptors beforethey are contacted with the double stranded polynucleotide and MuAtransposase.

Uncoupling

The method of the invention may involve characterising multiple targetpolynucleotides and uncoupling of the at least the first targetpolynucleotide.

In a preferred embodiment, the invention involves characterising two ormore target polynucleotides. The method comprises:

-   -   (a) providing a first polynucleotide in a first sample;    -   (b) providing a second polynucleotide in a second sample;    -   (c) coupling the first polynucleotide in the first sample to a        membrane using one or more anchors;    -   (d) contacting the first polynucleotide with a pore of the        invention such that the polynucleotide moves with respect to,        such as through, the pore;    -   (e) taking one or more measurements as the first polynucleotide        moves with respect to the pore wherein the measurements are        indicative of one or more characteristics of the first        polynucleotide and thereby characterising the first        polynucleotide;    -   (f) uncoupling the first polynucleotide from the membrane;    -   (g) coupling the second polynucleotide in the second sample to        the membrane using one or more anchors;    -   (h) contacting the second polynucleotide with the pore of the        invention such that the second polynucleotide moves with respect        to, such as through, the pore; and    -   (i) taking one or more measurements as the second polynucleotide        moves with respect to the pore wherein the measurements are        indicative of one or more characteristics of the second        polynucleotide and thereby characterising the second        polynucleotide.

This type of method is discussed in detail in the UK Application No.1406155.0.

Step (f) (i.e. uncoupling of the first polynucleotide) may be performedbefore step (g) (i.e. before coupling the second polynucleotide to themembrane). Step (g) may be performed before step (f). If the secondpolynucleotide is coupled to the membrane before the firstpolynucleotide is uncoupled, step (f) preferably comprises selectivelyuncoupling the first polynucleotide from the membrane (i.e. uncouplingthe first polynucleotide but not the second polynucleotide from themembrane). A skilled person can design a system in which selectiveuncoupling is achieved. Steps (f) and (g) may be performed at the sametime. This is discussed in more detail below.

In step (f), at least 10% of the first polynucleotide is preferablyuncoupled from the membrane. For instance, at least 20%, at least 30%,at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90% or at least 95% of the first polynucleotide may be uncoupledfrom the membrane. Preferably, all of the first polynucleotide isuncoupled from the membrane. The amount of the first polynucleotideuncoupled from the membrane can be determined using the pore. This isdisclosed in the Examples.

The first polynucleotide and second polynucleotide may be different fromone another. Alternatively, the first and second polynucleotides may bedifferent polynucleotides. In such instances, there may be no need toremove at least part of the first sample before adding the secondpolynucleotide. This is discussed in more detail below. If the methodconcerns investigating three or more polynucleotides, they may all bedifferent from one another or some of them may be different from oneanother.

The first polynucleotide and the second polynucleotide may be twoinstances of the same polynucleotide. The first polynucleotide may beidentical to the second polynucleotide. This allows proof reading. Ifthe method concerns investigating three or more polynucleotides, theymay all be three or more instances of the same polynucleotide or some ofthem may be separate instances of the same polynucleotide.

The first sample and second sample may be different from one another.For instance, the first sample may be derived from a human and thesecond sample may be derived from a virus. If the first and secondsamples are different from one another, they may contain or be suspectedof containing the same first and second polynucleotides. If the methodconcerns investigating three or more samples, they may all be differentfrom one another or some of them may be different from one another.

The first sample and the second sample are preferably two instances ofthe same sample. The first sample is preferably identical to the secondsample. This allows proof reading. If the method concerns investigatingthree or more samples, they may all be three or more instances of thesame sample or some of them may be separate instances of the samesample.

Any number of polynucleotides can be investigated. For instance, themethod of the invention may concern characterising 3, 4, 5, 6, 7, 8, 9,10, 20, 30, 50, 100 or more polynucleotides. If three or morepolynucleotides are investigated using the method of the invention, thesecond polynucleotide is also uncoupled from the membrane and therequisite number of steps are added for the third polynucleotide. Thesame is true for four or more polynucleotides.

The method of the invention involves uncoupling the first polynucleotidefrom the membrane. The method of the invention may involve uncouplingthe second polynucleotide from the membrane if three or morepolynucleotides are being investigated.

The first polynucleotide can be uncoupled from the membrane using anyknown method. The first polynucleotide is preferably not uncoupled fromthe membrane in step (f) using the transmembrane pore. The firstpolynucleotide is preferably not uncoupled from the membrane using avoltage or an applied potential.

Step (f) preferably comprises uncoupling the first polynucleotide fromthe membrane by removing the one or more anchors from the membrane. Ifthe anchors are removed, the second polynucleotide is coupled to themembrane using other (or separate) anchors. The anchors used to couplethe second polynucleotide may be the same type of anchors used to couplethe first polynucleotide or different type of anchors.

Step (f) more preferably comprises contacting the one or more anchorswith an agent which has a higher affinity for the one or more anchorsthan the anchors have for the membrane. A variety of protocols forcompetitive binding or immunoradiometric assays to determine thespecific binding capability of molecules are well known in the art (seefor example Maddox et al, J. Exp. Med. 158, 1211-1226, 1993). The agentremoves the anchor(s) from the membrane and thereby uncouples the firstpolynucleotide. The agent is preferably a sugar. Any sugar which bindsto the one or more anchors with a higher affinity than the one or moreanchors have for the membrane may be used. The sugar may be acyclodextrin or derivative thereof as discussed below.

If one or more anchors comprise a hydrophobic anchor, such ascholesterol, the agent is preferably a cyclodextrin or a derivativethereof or a lipid. The cyclodextrin or derivative thereof may be any ofthose disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J. Am.Chem. Soc. 116, 6081-6088. The agent is more preferablyheptakis-6-amino-β-cyclodextrin (am₁-βCD),6-monodeoxy-6-monoamino-β-cyclodextrin (am₁-βCD) orheptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu₇-βCD). Any of the lipidsdisclosed herein may be used.

If an anchor comprise(s) streptavidin, biotin or desthiobiotin, theagent is preferably biotin, desthiobiotin or streptavidin. Both biotinand desthiobiotin bind to streptavidin with a higher affinity thanstreptavidin binds to the membrane and vice versa. Biotin has a strongeraffinity for streptavidin than desthiobiotin. An anchor comprisingstreptavidin may therefore be removed from the membrane using biotin orstreptavidin and vice versa.

If an anchor comprises a protein, the agent is preferably an antibody orfragment thereof which specifically binds to the protein. An antibodyspecifically binds to a protein if it binds to the protein withpreferential or high affinity, but does not bind or binds with only lowaffinity to other or different proteins. An antibody binds withpreferential or high affinity if it binds with a Kd of 1×10⁻⁶ M or less,more preferably 1×10⁻⁷ M or less, 5×10⁻⁸ M or less, more preferably1×10⁻⁸ M or less or more preferably 5×10⁻⁹ M or less. An antibody bindswith low affinity if it binds with a Kd of 1×10⁻⁶ M or more, morepreferably 1×10⁻⁵ M or more, more preferably 1×10⁻⁴ M or more, morepreferably 1×10⁻³ M or more, even more preferably 1×10⁻² M or more. Anymethod may be used to detect binding or specific binding. Methods ofquantitatively measuring the binding of an antibody to a protein arewell known in the art. The antibody may be a monoclonal antibody or apolyclonal antibody. Suitable fragments of antibodies include, but arenot limited to, Fv, F(ab′) and F(ab′)₂ fragments, as well as singlechain antibodies. Furthermore, the antibody or fragment thereof may be achimeric antibody or fragment thereof, a CDR-grafted antibody orfragment thereof or a humanised antibody or fragment thereof.

Step (f) preferably comprises contacting the one or more anchors with anagent which reduces ability of the one or more anchors to couple to themembrane. For instance, the agent could interfere with the structureand/or hydrophobicity of the one or more anchors and thereby reducetheir ability to couple to the membrane. If an anchor comprisescholesterol, the agent is preferably cholesterol dehydrogenase. If ananchor comprises a lipid, the agent is preferably a phospholipase. If ananchor comprises a protein, the agent is preferably a proteinase orurea. Other combination of suitable anchors and agents will be clear toa person skilled in the art.

Step (f) preferably comprises uncoupling the first polynucleotide fromthe membrane by separating the first polynucleotide from the one or moreanchors. This can be done in any manner. For instance, the linker couldbe cut in an anchor comprising a linker. This embodiment is particularlyapplicable to anchors which involve linkage via hybridisation. Suchanchors are discussed above.

Step (f) more preferably comprises uncoupling the first polynucleotidefrom the membrane by contacting the first polynucleotide and the one ormore anchors with an agent which competes with the first polynucleotidefor binding to one or more anchors. Methods for determining andmeasuring competitive binding are known in the art. The agent ispreferably a polynucleotide which competes with the first polynucleotidefor hybridisation to the one or more anchors. For instance, if the firstpolynucleotide is coupled to the membrane using one or more anchorswhich involve hybridisation, the polynucleotide can be uncoupled bycontacting the one or more anchors with a polynucleotide which alsohybridises to the site of hybridisation. The polynucleotide agent istypically added at a concentration that is higher than the concentrationof the first polynucleotide and one or more anchors. Alternatively, thepolynucleotide agent may hybridise more strongly to the one or moreanchors than the first polynucleotide.

Step (f) more preferably comprises (i) contacting the firstpolynucleotide and the one or more anchors with urea,tris(2-carboxyethyl)phosphine (TCEP), dithiothreitol (DTT), streptavidinor biotin, UV light, an enzyme or a binding agent; (ii) heating thefirst polynucleotide and the one or more anchors; or (iii) altering thepH. Urea, tris(2-carboxyethyl)phosphine (TCEP) or dithiothreitol (DTT)are capable of disrupting anchors and separating the firstpolynucleotide from the membrane. If an anchor comprises astreptavidin-biotin link, then a streptavidin agent will compete forbinding to the biotin. If an anchor comprises astreptavidin-desthiobiotin link, then a biotin agent will compete forbinding to the streptavidin. UV light can be used to breakdownphotolabile groups. Enzymes and binding agents can be used to cut,breakdown or unravel the anchor. Preferred enzymes include, but are notlimited to, an exonuclease, an endonuclease or a helicase. Preferredbinding agents include, but are not limited to, an enzyme, an antibodyor a fragment thereof or a single-stranded binding protein (SSB). Any ofthe enzymes discussed below or antibodies discussed above may be used.Heat and pH can be used to disrupt hybridisation and other linkages.

If the first polynucleotide is uncoupled from the membrane by separatingthe first polynucleotide from the one or more anchors, the one or moreanchors will remain in the membrane. Step (g) preferably comprisescoupling the second polynucleotide to the membrane using the one or moreanchors that was separated from the first polynucleotide. For instance,the second polynucleotide may also be provided with one or morepolynucleotides which hybridise(s) to the one or more anchors thatremain in the membrane. Alternatively, step (g) preferably comprisescoupling the second polynucleotide to the membrane using one or moreseparate anchors from the ones separated from the first polynucleotide(i.e. one or more other anchors). The one or more separate anchors maybe the same type of anchors used to couple the first polynucleotide tothe membrane or may be different types of anchors. Step (g) preferablycomprises coupling the second polynucleotide to the membrane using oneor more different anchors from the one or more anchors separated fromthe first polynucleotide.

In a preferred embodiment, steps (f) and (g) comprise uncoupling thefirst polynucleotide from the membrane by contacting the membrane withthe second polynucleotide such that the second polynucleotide competeswith the first polynucleotide for binding to the one or more anchors andreplaces the first polynucleotide. For instance, if the firstpolynucleotide is coupled to the membrane using one or more anchorswhich involve hybridisation, the first polynucleotide can be uncoupledby contacting the anchors with the second polynucleotide attached topolynucleotides which also hybridise to the sites of hybridisation inthe one or more anchors. The second polynucleotide is typically added ata concentration that is higher than the concentration of the firstpolynucleotide and the one or more anchors. Alternatively, the secondpolynucleotide may hybridise more strongly to the one or more anchorsthan the first polynucleotide.

Removal or Washing

Although the first polynucleotide is uncoupled from the membrane in step(f), it is not necessarily removed or washed away. If the secondpolynucleotide can be easily distinguished from the firstpolynucleotide, there is no need to remove the first polynucleotide.

Between steps (f) and (g), the method preferably further comprisesremoving at least some of the first sample from the membrane. At least10% of the first sample may be removed, such as at least 20%, at least30%, at least 40%, at least 50%, at least 60%, at least 70%, at least80% or at least 90% of the first sample may be removed.

The method more preferably further comprises removing all of the firstsample from the membrane. This can be done in any way. For instance, themembrane can be washed with a buffer after the first polynucleotide hasbeen uncoupled. Suitable buffers are discussed below.

Modified Polynucleotides

Before characterisation, a target polynucleotide may be modified bycontacting the polynucleotide with a polymerase and a population of freenucleotides under conditions in which the polymerase forms a modifiedpolynucleotide using the target polynucleotide as a template, whereinthe polymerase replaces one or more of the nucleotide species in thetarget polynucleotide with a different nucleotide species when formingthe modified polynucleotide. The modified polynucleotide may then beprovided with one or more helicases attached to the polynucleotide andone or more molecular brakes attached to the polynucleotide. This typeof modification is described in UK Application No. 1403096.9. Any of thepolymerases discussed above may be used. The polymerase is preferablyKlenow or 90 North.

The template polynucleotide is contacted with the polymerase underconditions in which the polymerase forms a modified polynucleotide usingthe template polynucleotide as a template. Such conditions are known inthe art. For instance, the polynucleotide is typically contacted withthe polymerase in commercially available polymerase buffer, such asbuffer from New England Biolabs®. The temperature is preferably from 20to 37° C. for Klenow or from 60 to 75° C. for 90 North. A primer or a 3′hairpin is typically used as the nucleation point for polymeraseextension.

Characterisation, such as sequencing, of a polynucleotide using atransmembrane pore typically involves analyzing polymer units made up ofk nucleotides where k is a positive integer (i.e. ‘k-mers’). This isdiscussed in International Application No. PCT/GB2012/052343 (publishedas WO 2013/041878). While it is desirable to have clear separationbetween current measurements for different k-mers, it is common for someof these measurements to overlap. Especially with high numbers ofpolymer units in the k-mer, i.e. high values of k, it can becomedifficult to resolve the measurements produced by different k-mers, tothe detriment of deriving information about the polynucleotide, forexample an estimate of the underlying sequence of the polynucleotide.

By replacing one or more nucleotide species in the target polynucleotidewith different nucleotide species in the modified polynucleotide, themodified polynucleotide contains k-mers which differ from those in thetarget polynucleotide. The different k-mers in the modifiedpolynucleotide are capable of producing different current measurementsfrom the k-mers in the target polynucleotide and so the modifiedpolynucleotide provides different information from the targetpolynucleotide. The additional information from the modifiedpolynucleotide can make it easier to characterise the targetpolynucleotide. In some instances, the modified polynucleotide itselfmay be easier to characterise. For instance, the modified polynucleotidemay be designed to include k-mers with an increased separation or aclear separation between their current measurements or k-mers which havea decreased noise.

The polymerase preferably replaces two or more of the nucleotide speciesin the target polynucleotide with different nucleotide species whenforming the modified polynucleotide. The polymerase may replace each ofthe two or more nucleotide species in the target polynucleotide with adistinct nucleotide species. The polymerase may replace each of the twoor more nucleotide species in the target polynucleotide with the samenucleotide species.

If the target polynucleotide is DNA, the different nucleotide species inthe modified typically comprises a nucleobase which differs fromadenine, guanine, thymine, cytosine or methylcytosine and/or comprises anucleoside which differs from deoxyadenosine, deoxyguanosine, thymidine,deoxycytidine or deoxymethylcytidine. If the target polynucleotide isRNA, the different nucleotide species in the modified polynucleotidetypically comprises a nucleobase which differs from adenine, guanine,uracil, cytosine or methylcytosine and/or comprises a nucleoside whichdiffers from adenosine, guanosine, uridine, cytidine or methylcytidine.The different nucleotide species may be any of the universal nucleotidesdiscussed above.

The polymerase may replace the one or more nucleotide species with adifferent nucleotide species which comprises a chemical group or atomabsent from the one or more nucleotide species. The chemical group maybe a propynyl group, a thio group, an oxo group, a methyl group, ahydroxymethyl group, a formyl group, a carboxy group, a carbonyl group,a benzyl group, a propargyl group or a propargylamine group.

The polymerase may replace the one or more nucleotide species with adifferent nucleotide species which lacks a chemical group or atompresent in the one or more nucleotide species. The polymerase mayreplace the one or more of the nucleotide species with a differentnucleotide species having an altered electronegativity. The differentnucleotide species having an altered electronegativity preferablycomprises a halogen atom.

The method preferably further comprises selectively removing thenucleobases from the one or more different nucleotides species in themodified polynucleotide.

Analyte Delivery

The target analyte is preferably attached to a microparticle whichdelivers the analyte towards the membrane. This type of delivery isdisclosed in UK Application No. 1418469.1. Any type of microparticle andattachment method may be used.

Other Characterisation Method

In another embodiment, a polynucleotide is characterised by detectinglabelled species that are added to the target polynucleotide by apolymerase and then released. The polymerase uses the polynucleotide asa template. Each labelled species is specific for each nucleotide. Thepolynucleotide is contacted with a pore of the invention, such as a poreof the invention, a polymerase and labelled nucleotides such thatphosphate labelled species are sequentially added to the thepolynucleotide by the polymerase, wherein the phosphate species containa label specific for each nucleotide. The labelled species may bedetected using the pore before they are released from the nucleotides(i.e. as they are added to the target polynucleotide) or after they arereleased from the nucleotides.

The polymerase may be any of those discussed above. The phosphatelabelled species are detected using the pore and thereby characterisingthe polynucleotide. This type of method is disclosed in EuropeanApplication No. 13187149.3 (published as EP 2682460). Any of theembodiments discussed above equally apply to this method.

Examples of labelled species include, but are not limited to, polymers,polyethylene gycols, sugars, cyclodextrins, fluorophores, drugs,metabolites, peptides. A non-limiting example of such tags can be foundin the work of Kumar et al. Sci Rep. 2012; 2:684. Epub 2012 Sep. 21.

Methods of Forming Sensors

The invention also provides a method of forming a sensor forcharacterising a target polynucleotide. The method comprises forming acomplex between a pore of the invention and a polynucleotide bindingprotein, such as a helicase or an exonuclease. The complex may be formedby contacting the pore and the protein in the presence of the targetpolynucleotide and then applying a potential across the pore. Theapplied potential may be a chemical potential or a voltage potential asdescribed above. Alternatively, the complex may be formed by covalentlyattaching the pore to the protein. Methods for covalent attachment areknown in the art and disclosed, for example, in InternationalApplication Nos. PCT/GB09/001679 (published as WO 2010/004265) andPCT/GB10/000133 (published as WO 2010/086603). The complex is a sensorfor characterising the target polynucleotide. The method preferablycomprises forming a complex between a pore of the invention and ahelicase. Any of the embodiments discussed above equally apply to thismethod.

The invention also provides a sensor for characterising a targetpolynucleotide. The sensor comprises a complex between a pore of theinvention and a polynucleotide binding protein. Any of the embodimentsdiscussed above equally apply to the sensor of the invention.

Kits

The present invention also provides a kit for characterising a targetpolynucleotide. The kit comprises a pore of the invention and thecomponents of a membrane. The membrane is preferably formed from thecomponents. The pore is preferably present in the membrane. The kit maycomprise components of any of the membranes disclosed above, such as anamphiphilic layer or a triblock copolymer membrane.

The kit may further comprise a polynucleotide binding protein. Any ofthe polynucleotide binding proteins discussed above may be used.

The kit may further comprise one or more anchors for coupling thepolynucleotide to the membrane.

The kit is preferably for characterising a double strandedpolynucleotide and preferably comprises a Y adaptor and a hairpin loopadaptor. The Y adaptor preferably has one or more helicases attached andthe hairpin loop adaptor preferably has one or more molecular brakesattached. The Y adaptor preferably comprises one or more first anchorsfor coupling the polynucleotide to the membrane, the hairpin loopadaptor preferably comprises one or more second anchors for coupling thepolynucleotide to the membrane and the strength of coupling of thehairpin loop adaptor to the membrane is preferably greater than thestrength of coupling of the Y adaptor to the membrane.

The kit of the invention may additionally comprise one or more otherreagents or instruments which enable any of the embodiments mentionedabove to be carried out. Such reagents or instruments include one ormore of the following: suitable buffer(s) (aqueous solutions), means toobtain a sample from a subject (such as a vessel or an instrumentcomprising a needle), means to amplify and/or express polynucleotides orvoltage or patch clamp apparatus. Reagents may be present in the kit ina dry state such that a fluid sample resuspends the reagents. The kitmay also, optionally, comprise instructions to enable the kit to be usedin the method of the invention or details regarding for which organismthe method may be used.

Apparatus

The invention also provides an apparatus for characterising a targetanalyte, such as a target polynucleotide. The apparatus comprises aplurality of pores of the invention and a plurality of membranes. Theplurality of pores are preferably present in the plurality of membranes.The number of pores and membranes is preferably equal. Preferably, asingle pore is present in each membrane.

The apparatus preferably further comprises instructions for carrying outthe method of the invention. The apparatus may be any conventionalapparatus for analyte analysis, such as an array or a chip. Any of theembodiments discussed above with reference to the methods of theinvention are equally applicable to the apparatus of the invention. Theapparatus may further comprise any of the features present in the kit ofthe invention.

The apparatus is preferably set up to carry out the method of theinvention.

The apparatus preferably comprises:

a sensor device that is capable of supporting the plurality of pores andmembranes and being operable to perform analyte characterisation usingthe pores and membranes; and

at least one port for delivery of the material for performing thecharacterisation.

Alternatively, the apparatus preferably comprises:

a sensor device that is capable of supporting the plurality of pores andmembranes being operable to perform analyte characterisation using thepores and membranes; and

at least one reservoir for holding material for performing thecharacterisation.

The apparatus more preferably comprises:

a sensor device that is capable of supporting the membrane and pluralityof pores and membranes and being operable to perform analytecharacterising using the pores and membranes;

at least one reservoir for holding material for performing thecharacterising;

a fluidics system configured to controllably supply material from the atleast one reservoir to the sensor device; and

one or more containers for receiving respective samples, the fluidicssystem being configured to supply the samples selectively from one ormore containers to the sensor device.

The apparatus may be any of those described in International ApplicationNo. No. PCT/GB08/004127 (published as WO 2009/077734), PCT/GB10/000789(published as WO 2010/122293), International Application No.PCT/GB10/002206 (published as WO 2011/067559) or InternationalApplication No. PCT/US99/25679 (published as WO 00/28312).

The following Example illustrates the invention.

Example 1

This Example describes the simulations which were run to investigate DNAbehaviour within CsgG.

Materials and Methods

Steered molecular dynamics simulations were performed to investigate themagnitude of the energetic barrier of CsgG-Eco and various mutants toDNA translocation. Simulations were performed using the GROMACS packageversion 4.0.5, with the GROMOS 53a6 forcefield and the SPC water model.The structure of CsgG-Eco (SEQ ID NO: 2) was taken from the protein databank, accession code 4UV3. In order to make models of the CsgG-Ecomutants, the wild-type protein structure was mutated using PyMOL. Themutants studied were CsgG-Eco-(F56A) (SEQ ID NO: 2 with mutation F56A),CsgG-Eco-(F56A-N55S) (SEQ ID NO: 2 with mutations F56A/N55S) andCsgG-Eco-(F56A-N55S-Y51A) (SEQ ID NO: 2 with mutations F56A/N55S/Y51A).

DNA was then placed into the pores. Two different systems were set up:

-   -   i. A single guanine nucleotide was placed into the pore, just        above the constriction region (approximately 5-10 Angstroms        above the residue 56 ring)    -   ii. A single strand of DNA (ssDNA) was placed along the pore        axis, with the 5′ end towards the beta-barrel side of the pore.        In this set up, the ssDNA was pre-threaded through the entire        length of the pore.

The simulation box was then solvated and then energy minimised using thesteepest descents algorithm.

Each system was simulated in the NPT ensemble, using the Berendsenthermostat and Berendsen barostat to 300 K. Throughout the simulation,restraints were applied to the backbone of the pore.

In order to pull the DNA through the pore, a pulling force was appliedto the phosphorus atom in the single guanine simulations. In the ssDNAsimulations the pulling force was applied to the phosphorus atom at the5′ end of the strand. The pulling force was applied at a constantvelocity by connecting a spring between the DNA phosphorus atommentioned above and an imaginary point travelling at a constant velocityparallel to the pore axis. Note that the spring does not have any shapenor does it undergo any hydrodynamic drag. The spring constant was equalto 5 kJmol⁻¹ Å⁻².

Results Single G Translocation

As shown in FIG. 3, a plot of the pulling force versus time shows thatthere is a large barrier for nucleotide entry into the ring ofphenylalanine residues F56 in the wild type CsgG-Eco pore. There was nosignificant barrier to guanine translocation observed for the CsgG-Ecomutants studied.

ssDNA Translocation

For ssDNA translocation, two simulations were run per pore with each runhaving a different applied pulling velocity (100 Å/ns and 10 Å/ns). Asshown in FIG. 4, which illustrates the faster pulling velocitysimulations, the CsgG wild-type pore required the largest pulling forceto enable ssDNA translocation. As shown in FIG. 5, which illustrates theslower pulling velocity simulations, both the CsgG-Eco (wild-type, SEQID NO: 2) and CsgG-Eco-(F56A) pores required the largest applied forceto enable ssDNA translocation. Comparisons between the pulling forcerequired for ssDNA translocation through CsgG and MspA baseline pore,suggest that mutation of the CsgG pore is required to allow a similarlevel of ssDNA translocation.

Example 2

This Example describes the characterisation of several CsgG mutants.

Materials and Methods

Prior to setting up the experiment, DNA construct X (final concentration0.1 nM, see FIG. 13 for cartoon representation of construct X anddescription) was pre-incubated at room temperature for five minutes withT4 Dda-E94C/C109A/C136A/A360C (SEQ ID NO: 24 with mutationsE94C/C109A/C136A/A360C, final concentration added to the nanopore system10 nM, which was provided in buffer (151.5 mM KCl, 25 mM potassiumphosphate, 5% glycerol, pH 7.0, 1 mM EDTA)). After five minutes, TMAD(100 μM) was added to the pre-mix and the mixture incubated for afurther 5 minutes. Finally, MgCl2 (1.5 mM final concentration added tothe nanopore system), ATP (1.5 mM final concentration added to thenanopore system), KCl (500 mM final concentration added to the nanoporesystem) and potassium phosphate buffer (25 mM final concentration addedto the nanopore system) were added to the pre-mix.

Electrical measurements were acquired from a variety of single CsgGnanopores inserted in block co-polymer in buffer (25 mM K Phosphatebuffer, 150 mM Potassium Ferrocyanide (II), 150 mM PotassiumFerricyanide (III), pH 8.0). After achieving a single pore inserted inthe block co-polymer, then buffer (2 mL, 25 mM K Phosphate buffer, 150mM Potassium Ferrocyanide (II), 150 mM Potassium Ferricyanide (III), pH8.0) was flowed through the system to remove any excess CsgG nanopores.150 uL of 500 mM KCl, 25 mM K Phosphate, 1.5 mM MgCl2, 1.5 mM ATP, pH8.0was then flowed through the system. After 10 minutes a 150 uL of 500 mMKCl, 25 mM potassium phosphate, 1.5 mM MgCl2, 1.5 mM ATP, pH8.0 wasflowed through the system and then the enzyme (T4Dda-E94C/C109A/C136A/A360C, 10 nM final concentration), DNA construct X(0.1 nM final concentration), fuel (MgCl2 1.5 mM final concentration,ATP 1.5 mM final concentration) pre-mix (150 μL total) was then flowedinto the single nanopore experimental system. The experiment was run at−120 mV and helicase-controlled DNA movement monitored.

Results Pores Showing Increased Range (FIGS. 6 to 8, and 18 to 30)

CsgG-Eco-(StrepII(C)) (SEQ ID NO: 2 where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus) has a range of 10 pA (see FIG. 6(a))whereas the CsgG-Eco pore mutants below exhibited an increased currentrange—1—CsgG-Eco-(Y51N-F56A-D149N-E185R-E201N-E203N-StrepII(C))9 (SEQ ID NO: 2with mutations Y51N/F56A/D149N/E185R/E201N/E203N where StrepII(C) is SEQID NO: 47 and is attached at the C-terminus) exhibited a range of 30 pA(See FIG. 6(b)).2—CsgG-Eco-(N55A-StrepII(C))9 (SEQ ID NO: 2 with mutation N55A whereStrepII(C) is has SEQ ID NO: 47 and is attached at the C-terminus)exhibited a range of ˜35 pA (see FIG. 6(c)).3—CsgG-Eco-(N55S-StrepII(C))9 (SEQ ID NO: 2 with mutations N55S whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) exhibiteda range of ˜40 pA (see FIG. 7(a)).4—CsgG-Eco-(Y51N-StrepII(C))9 (SEQ ID NO: 2 with mutation Y51N whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) exhibiteda range of ˜40 pA (see FIG. 7(b)).5—CsgG-Eco-(Y51A-F56A-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56A where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜30 pA (see FIG. 7(c)).6—CsgG-Eco-(Y51A-F56N-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56N where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜20 pA (see FIG. 8(a)).7—CsgG-Eco-(Y51A-N55S-F56A-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/N55S/F56A where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜30 pA (see FIG. 8(b)).8—CsgG-Eco-(Y51A-N55S-F56N-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/N55S/F56N where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜30 pA (see FIG. 8(c)).13—CsgG-Eco-(F56H-StrepII(C))9 (SEQ ID NO: 2 with mutation F56H whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) exhibiteda range of ˜35 pA (see FIG. 18).14—CsgG-Eco-(F56Q-StrepII(C))9 (SEQ ID NO: 2 with mutation F56Q whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) exhibiteda range of ˜40 pA (see FIG. 19).15—CsgG-Eco-(F56T-StrepII(C))9 (SEQ ID NO: 2 with mutation F56T whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) exhibiteda range of ˜35 pA (see FIG. 20).16—CsgG-Eco-(S54P/F56A-StrepII(C))9 (SEQ ID NO: 2 with mutationS54P/F56A where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜35 pA (see FIG. 21).17—CsgG-Eco-(Y51T/F56A-StrepII(C))9 (SEQ ID NO: 2 with mutationY51T/F56A where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜30 pA (see FIG. 22).18—CsgG-Eco-(F56P-StrepII(C))9 (SEQ ID NO: 2 with mutation F56P whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) exhibiteda range of ˜30 pA (see FIG. 23).19—CsgG-Eco-(F56A-StrepII(C))9 (SEQ ID NO: 2 with mutation F56A whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) exhibiteda range of ˜40 pA (see FIG. 24).20 CsgG-Eco-(Y51T/F56Q-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51T/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜30 pA (see FIG. 25).21 CsgG-Eco-(N55S/F56Q-StrepII(C))9 (SEQ ID NO: 2 with mutationsN55S/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜35 pA (see FIG. 26).22 CsgG-Eco-(Y51T/N55S/F56Q-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51T/N55S/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜35 pA (see FIG. 27).23 CsgG-Eco-(F56Q/N102R-StrepII(C))9 (SEQ ID NO: 2 with mutationsF56Q/N102R where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜30 pA (see FIG. 28).24 CsgG-Eco-(Y51Q/F56Q-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51Q/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜40 pA (see FIG. 29).25 CsgG-Eco-(Y51A/F56Q-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) exhibited a range of ˜35 pA (see FIG. 30).

Pores Showing Increased Throughput (FIGS. 9 and 10)

As can be seen from FIGS. 9 and 10, the following mutant pores (9-12below) exhibited multiple helicase controlled DNA movements (Labelled asX in FIGS. 9 and 10) per channel in 4 hours, whereasCsgG-Eco-(StrepII(C)) (SEQ ID NO: 2 where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus) shown in FIG. 9(a) frequentlyexhibited only 1 or 2 helicase controlled DNA movements (labelled as Xin FIG. 9(a)) per channel in 4 hours and instead exhibited prolongedblock regions (labelled as Y in FIG. 9(a)).

9—CsgG-Eco-(D149N-E185N-E203N-StrepII(C))9 (SEQ ID NO: 2 with mutationsD149N/E185N/E203N where StrepII(C) is SEQ ID NO: 47 and is attached atthe C-terminus) (FIG. 9(b))10—CsgG-Eco-(D149N-E185N-E201N-E203N-StrepII(C))9 (SEQ ID NO: 2 withmutations D149N/E185N/E201N/E203N where StrepII(C) is SEQ ID NO: 47 andis attached at the C-terminus) (FIG. 9(c))11—CsgG-Eco-(D149N-E185R-D195N-E201N-E203N)-StrepII(C))9 (SEQ ID NO: 2with mutations D149N/E185R/D195N/E201N/E203N where StrepII(C) is SEQ IDNO: 47 and is attached at the C-terminus) (FIG. 10(a))12—CsgG-Eco-(D149N-E185R-D195N-E201R-E203N)-StrepII(C))9 (SEQ ID NO: 2with mutations D149N/E185R/D195N/E201R/E203N where StrepII(C) is SEQ IDNO: 47 and is attached at the C-terminus) (FIG. 10(b))

Pore Showing Increased Insertion (FIGS. 11 and 12)

As can be seen by comparing FIGS. 11 and 12, the mutant poreCsgG-Eco-(T150I-StrepII(C))9 (SEQ ID NO: 2 with mutations T150I whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) shown inFIG. 12. was present in the membrane in increased pore numbers (˜4-5fold) compared with the CsgG-Eco-(StrepII(C)) (SEQ ID NO: 2 whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus) pore(shown in FIG. 11). Arrows in FIGS. 11 and 12 illustrated the number ofCsgG-Eco nanopores which inserted into the block co-polymer in a 4 hourexperiment (130-140 in FIGS. 11 and 1-11 in FIG. 12 each corresponded toa separate nanopore experiment). For CsgG-Eco-(StrepII(C)) (SEQ ID NO: 2where StrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus)three experiments showed insertion of one nanopore, whereas for themutant pore (CsgG-Eco-(T150I-StrepII(C))9) each experiment showedinsertion of at least one nanopore and several experiments showedmultiple pore insertions.

Example 3

This example described an E. Coli purification method developed topurify the CsgG pore.

Materials and Methods

DNA encoding the polypeptide Pro-CsgG-Eco-(StrepII(C)) (SEQ ID NO: 2where StrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus andwhere Pro is SEQ ID NO: 48 and is attached at the N-terminus) wassynthesised in GenScript USA Inc. and cloned into a pT7 vectorcontaining ampicillin resistance gene. Protein expression of the pT7vector was induced by Isopropyl β-D-1-thiogalactopyranoside (IPTG). Theconcentration of the DNA solution was adjusted to 400 ng/uL. DNA (10)was used to transform Lemo21(DE3) competent E. coli cells (500, NEB,catalogue number C2528H). Prior to transformation, the CsgG gene wasknocked out from Lemo21(DE3) cells (Gene Bridges GmbH, Germany). Thecells were then plated out on LB agar containing ampicillin (0.1 mg/mL)and incubated for approx 16 hours at 37° C.

Bacterial colonies grown on LB plates, containing ampicillin,incorporated the CsgG plasmid. One such colony was used to inoculate astarter culture of LB media (100 mL) containing carbenicillin (0.1mg/mL). The starter culture was grown at 37° C. with agitation untilOD600 was reached to 1.0-1.2. The starter culture was used to inoculatea fresh 500 mL of LB media containing carbenicillin (0.1 mg/mL) andRhamnose (500 μM) to an O.D. 600 of 0.1. The culture was grown at 37° C.with agitation until OD600 reached 0.6. The temperature of the culturewas then adjusted to 18° C. and induction was initiated by the additionof IPTG (0.2 mM final concentration). Induction was carried out forapproximately 18 hours with agitation at 18° C.

Following induction, the culture was pelleted by centrifugation at 6,000g for 30 minutes. The pellet was resuspended in 50 mM Tris, 300 mM NaCl,containing protease inhibitors (Merck Millipore 539138), benzonasenuclease (Sigma E1014) and 1× bugbuster (Merck Millipore 70921) pH8.0(approximately 10 mL of buffer per gram of pellet). Suspension was mixedwell until it was fully homogeneous, the sample was then transferred toroller mixer at 4° c. for approx 5 hours. Lysate was pelleted bycentrifugation at 20,000 g for 45 minutes and the supernatant wasfiltered through 0.2204 PES syringe filter. Supernatant which containedCsgG (known as sample 1) was taken forward for purification by columnchromatography.

Sample 1 was applied to a 5 mL Strep Trap column (GE Healthcare). Thecolumn was washed with 25 mM Tris, 150 mM NaCl, 2 mM EDTA, 0.01% DDM pH8until a stable baseline of 10 column volumes was maintained. The columnwas then washed with 25 mM Tris, 2M NaCl, 2 mM EDTA, 0.01% DDM pH8before being returned to the 150 mM buffer. Elution was carried out with10 mM desthiobiotin. An example of a chromatography trace of Strep trap(GE Healthcare) purification of a CsgG protein is shown in FIG. 14. Theelution peak is labelled E1. FIG. 15 shows an example of a typicalSDS-PAGE visualization of CsgG-Eco protein after the initial Streppurification. Lanes 1-3 shows the main elution peak (labelled E1 in FIG.14) which contained CsgG protein as indicated by the arrow. Lanes 4-6corresponded to elution fractions of the tail of the main elution peak(labelled E1 in FIG. 14) which contained contaminants.

The elution peak was pooled and heated to 65° C. for 15 minutes toremove heat unstable contaminated proteins. The heated solution wassubjected to centrifugation at 20,000 g for 10 minutes and the pelletwas discarded. The supernatant was subjected to gel filtration on a 120mL Sephadex 5200 column (GE Healthcare) in 25 mM Tris, 150 mM NaCl, 2 mMEDTA, 0.01% DDM, 0.1% SDS pH8. Monitoring was carried out at 220 nM dueto low Tryptophan component of protein. The sample was eluted atapproximately 55 mL volume (FIG. 16 shows the size exclusion columntrace with the 55 mL sample peak labelled with a star). The elution peakwas run on a 4-20% TGX (see FIG. 17, Bio Rad) to confirm the presence ofthe pore of interest CsgG-Eco-(StrepII(C)) (SEQ ID NO: 2 whereStrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus).Identified fractions were pooled and concentrated by 50 kD Amicon spincolumn.

Example 4

This example describes the simulations which were run to investigate theinteraction between CsgG-Eco-(Y51T/F56Q)-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51T/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached atthe C-terminus pore mutant No. 20) with T4 Dda-(E94C/C109A/C136A/A360C)(SEQ ID NO: 24 with mutations E94C/C109A/C136A/A360C and then(ΔM1)G1G2).

Simulation Methods

Simulations were performed using the GROMACS package version 4.0.5, withthe GROMOS 53a6 forcefield and the SPC water model.The CsgG-Eco-(Y51T/F56Q)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51T/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus pore mutant No. 20) model was based on the crystal structuresof CsgG found in the protein data bank, accession codes 4UV3 and 4Q79.The relevant mutations were made using PyMOL. The resultant pore modelwas then energy minimised using the steepest descents algorithm. The T4Dda (E94C/C109A/C136A/A360C) (SEQ ID NO: 24 with mutationsE94C/C109A/C136A/A360C and then (ΔM1)G1G2) model was based on theDda1993 structure found in the protein data bank, accession code 3UPU.Again, relevant mutations were made using PyMOL, and the model wasenergy minimised using the steepest descents algorithm.

The T4 Dda-(E94C/C109A/C136A/A360C) (SEQ ID NO: 24 with mutationsE94C/C109A/C136A/A360C and then (ΔM1)G1G2) model was then placed aboveCsgG-Eco-(Y51T/F56Q)-StrepII(C))9 (SEQ ID NO: 2 with mutations Y51T/F56Qwhere StrepII(C) is SEQ ID NO: 47 and is attached at the C-terminus poremutant No. 20). Three simulations were performed with a differentinitial enzyme conformation (Runs 1 to 3 (0 ns), see FIG. 31):

In all enzyme conformations, the enzyme was oriented such that the 5′end of the DNA was pointing towards the pore, and the enzyme wasunrestrained throughout the simulation. The pore backbone was restrainedand the simulation box was solvated. The system was simulated in the NPTensemble for 40 ns, using the Berendsen thermostat and Berendsenbarostat to 300 K.The contacts between the enzyme and pore were analysed using bothGROMACS analysis software and also locally written code. The tablesbelow show the number of contacts observed for both pore and enzymeamino acids. Tables 6-8 shows the amino acid contact points on porewhich interact with the amino acid contact points on the enzyme. In twoout of the three simulations the enzyme tilts on top of the pore (seerun 2 and 3 (20, 30 and 40 ns), FIGS. 31 and 32). Run 1 shows that theenzyme has not tilted and so points that are shown to have highinteraction in table 6 can be optimised in order to increase enzymestability on the pore cap.

TABLE 6 run 1 enzyme and pore contact interactions Pore Enzyme #contacts ASN 102 ASP 198 8200 ASN 102 TYR 438 8130 GLN 100 ASP 212 7369GLU 101 TRP 195 5979 ARG 97 TYR 350 4873 GLU 101 LEU 215 4851 ASN 102TRP 195 3988 ARG 97 TYR 415 3798 GLU 101 TYR 350 3759 LEU 113 ASP 2123718 ASN 102 LYS 358 3124 ARG 97 GLY 211 2765 GLU 101 CYS 412 2715 ARG97 GLY 193 2708 ASN 102 ILE 196 2342 GLU 101 TYR 415 2268 GLU 101 ARG216 2158 ARG 110 THR 213 2094 ARG 110 ASP 212 2066 GLY 103 ARG 216 1456GLU 101 TYR 318 1333 ASN 102 GLU 347 1316 GLU 101 LYS 194 1310 ARG 97PRO 411 1203 GLU 101 LYS 358 1161 ASN 102 ARG 216 1132 ARG 97 TRP 195888 LYS 94 TYR 415 793 ASN 102 PRO 315 696 ASN 102 LYS 247 541 GLU 101ALA 214 449 ASN 102 ASP 346 440 ARG 97 ALA 214 366 ARG 97 LYS 194 336GLU 101 ASP 212 302 ARG 97 VAL 439 267 ARG 110 THR 210 263 ARG 97 THR210 259 ARG 97 GLN 422 257 GLU 101 TYR 409 228 ALA 98 TRP 195 207 GLU101 LYS 247 201 ASN 102 GLU 317 179 ARG 110 ARG 216 147 ARG 97 ASP 212108 ASN 102 VAL 314 87 GLU 101 THR 213 72 ASN 102 LYS 255 70 VAL 105 ARG216 69 ASN 102 LEU 215 59 ASN 102 THR 210 55 ILE 111 ASP 212 48 ARG 97HIS 414 48 THR 104 ARG 216 36 ASN 102 TYR 197 32 GLN 100 THR 213 30 ASN102 GLU 361 28 ARG 97 VAL 418 28 ALA 98 TYR 415 27 GLU 101 LEU 354 17GLU 101 TYR 197 16 ASN 102 GLY 316 16 ARG 97 GLU 361 16 ARG 97 GLU 34714 ILE 107 ARG 216 12 ASN 102 GLY 208 12 ARG 97 TYR 409 11 ARG 97 LYS247 11 GLU 101 LYS 364 8 ARG 97 PHE 209 7 LYS 94 GLU 419 6 GLU 101 PRO411 5 GLU 101 GLU 317 5 ASN 102 ILE 251 5 ARG 97 LEU 354 5 LYS 94 VAL418 3 ASN 102 ARG 321 3 ARG 97 LYS 243 3 LYS 94 CYS 412 2 LEU 113 THR210 2 GLY 103 GLU 317 2 GLU 101 LYS 351 2 ASN 102 TYR 318 2 ASN 102 MET219 2 ASN 102 LYS 194 2 ARG 97 VAL 314 2 ARG 97 LYS 364 2 THR 104 PRO315 1 GLY 103 THR 213 1 GLU 101 PRO 315 1

TABLE 7 run 2 enzyme and pore contact interactions Pore Enzyme #contacts GLU 101 THR 210 14155 SER 115 ASP 202 9477 ARG 97 THR 210 9064ASN 102 VAL 200 5323 THR 104 ASP 202 4476 ASN 102 ASN 221 3422 GLU 101PHE 437 3171 ARG 97 ASP 217 2698 GLU 101 ARG 216 2198 ARG 97 GLY 2081730 GLU 101 LYS 199 1710 SER 115 SER 224 1440 ASN 102 LYS 199 1351 ASN102 ASP 212 1298 ASN 102 ARG 405 1219 GLU 101 ARG 207 1180 ASN 102 SER224 1150 ASN 102 LYS 255 1114 ARG 97 ASP 198 946 GLU 101 PHE 209 931 ARG97 THR 213 791 ARG 97 ARG 216 599 ASN 102 THR 210 589 GLN 114 ASP 202530 ASN 102 ASP 202 492 ARG 97 ASP 212 490 GLY 103 ARG 405 474 THR 104SER 224 451 GLU 101 LYS 255 429 ASN 102 ASP 198 405 ASN 102 PHE 209 400ASN 102 ARG 178 316 ARG 110 GLU 258 309 ASN 102 ASN 180 257 GLN 100 PHE223 256 GLU 101 TYR 197 220 GLN 114 SER 228 212 LEU 113 PHE 223 210 ASN102 ILE 225 204 GLN 114 LYS 227 194 GLU 101 GLY 211 189 GLU 101 ASP 212174 LEU 113 SER 224 159 LEU 113 GLY 203 145 ARG 97 VAL 220 134 GLU 101THR 213 133 THR 104 SER 228 125 ARG 97 TYR 197 123 LYS 94 ASP 212 118ASN 102 ARG 216 110 ASN 102 ASN 235 108 ASN 102 GLY 211 104 GLU 101 ARG405 79 GLN 114 SER 224 69 ASN 102 VAL 220 63 LEU 113 LYS 227 49 ASN 102VAL 201 42 ARG 97 PHE 209 42 GLU 101 ASN 180 40 ARG 97 TYR 438 38 ARG 97ARG 207 32 ASN 102 PHE 407 28 SER 115 ASN 221 23 ARG 110 HIS 204 22 GLU101 PHE 223 21 ARG 97 ASP 189 19 ARG 110 PHE 223 16 THR 104 ILE 225 13GLY 103 ASN 180 11 ARG 97 LYS 194 11 GLU 101 PHE 407 10 ARG 97 MET 219 9THR 104 ASN 235 8 ARG 110 ARG 405 8 ARG 97 TRP 195 7 ILE 111 PHE 223 6GLU 101 GLY 208 6 LEU 113 ASP 202 5 GLU 101 ARG 178 5 ASN 102 THR 213 5ALA 98 ARG 216 5 ASN 102 ASP 217 4 ARG 97 LYS 199 4 THR 104 LEU 229 3THR 104 ARG 405 3 GLU 101 VAL 201 3 GLU 101 MET 219 3 ARG 110 ASP 202 3ARG 110 ARG 207 2 THR 104 VAL 201 1 GLY 103 SER 224 1 GLY 103 LYS 255 1GLY 103 GLU 258 1 GLY 103 ASN 235 1 GLU 101 ASP 198 1 ASN 102 PHE 437 1ARG 97 PHE 437 1 ARG 110 LYS 227 1

TABLE 8 run 3 enzyme and pore contact interactions Pore Enzyme #contacts ARG 97 THR 174 15557 GLN 100 ASP 5 10353 GLU 101 LYS 177 9238ARG 97 SER 179 6630 LEU 116 ASP 202 6545 GLU 101 TYR 434 6524 SER 115ASP 202 5693 GLU 101 HIS 204 5457 ARG 97 GLN 10 5106 ARG 93 ASP 202 4646ARG 93 GLU 8 4446 SER 115 LYS 11 4342 LEU 113 ASP 5 3871 ASN 102 SER 2243605 GLU 101 ASN 12 3344 GLU 101 GLN 10 3327 ARG 97 GLU 175 3096 GLU 101SER 224 3028 LEU 116 GLU 8 2936 LYS 94 ASP 185 2708 ARG 97 ASN 180 2700GLU 101 PHE 3 2500 THR 104 LYS 11 2352 SER 115 GLU 8 2323 ARG 93 ASN 1801912 ASN 102 LYS 177 1838 LYS 94 ASP 198 1828 ARG 110 ASP 5 1714 ALA 98GLY 203 1701 ASN 102 ASN 12 1695 GLU 101 TYR 169 1691 ARG 97 THR 7 1593ARG 110 ASP 4 1404 ARG 97 ASP 212 1381 ASN 102 HIS 204 1226 ASN 102 ASN15 1173 ARG 97 VAL 176 1096 ALA 98 HIS 204 998 ARG 97 ASP 202 875 ASN102 TYR 434 850 ALA 98 ASN 12 716 GLU 101 THR 213 702 GLU 101 ARG 178642 GLU 101 ASN 221 600 ASN 102 LYS 11 588 ARG 97 ASP 217 585 ARG 97 ARG207 537 GLU 101 ARG 207 525 ARG 97 PHE 437 511 GLU 101 ARG 216 510 ASN102 LYS 19 482 ARG 97 HIS 204 473 LEU 113 LYS 11 409 ARG 97 THR 213 358ARG 93 ASP 212 354 ARG 97 TYR 169 316 ARG 97 GLY 203 308 ARG 97 ASP 435300 GLN 87 LYS 199 249 THR 104 ASN 15 221 ARG 97 ALA 181 220 ASN 102 LYS227 198 LYS 94 ARG 178 184 ASN 102 GLU 8 183 LEU 113 LEU 6 182 ARG 93SER 179 179 LEU 90 ASN 180 172 LEU 90 ASP 202 144 ARG 97 ILE 225 138 GLU101 ASN 15 135 GLU 101 LYS 19 113 LYS 94 ASN 180 109 LYS 94 GLU 175 105ARG 93 THR 7 81 LYS 94 ARG 207 77 GLN 100 PHE 3 72 ASN 102 ARG 216 66ARG 97 LYS 177 62 GLU 101 THR 210 59 ARG 97 ARG 178 56 LYS 94 ASP 212 55ARG 97 GLU 172 53 GLU 101 VAL 176 51 ALA 98 ARG 207 49 ARG 110 PHE 3 48ALA 98 ASP 202 47 ARG 97 VAL 200 40 ALA 98 VAL 201 36 LYS 94 THR 210 35ILE 111 ASP 5 32 ARG 97 ARG 405 27 LEU 90 VAL 200 26 ARG 97 THR 210 26GLY 103 PHE 3 25 GLU 101 PHE 209 25 ARG 97 ARG 216 22 ASN 102 VAL 220 21LYS 94 GLY 211 19 ARG 97 PHE 209 17 GLU 101 LYS 227 15 GLN 114 LYS 11 15GLY 103 LYS 19 13 ARG 97 PHE 3 13 GLU 101 THR 2 12 GLU 101 ILE 225 12ARG 97 ILE 184 12 ALA 98 GLU 8 12 ALA 98 ARG 178 12 ASN 102 ILE 225 11LYS 94 LYS 199 10 GLU 101 ARG 433 8 ARG 97 ASN 221 8 LYS 94 VAL 200 7ASN 102 ASP 202 7 ASN 102 ASN 221 7 ARG 97 LEU 173 7 SER 115 HIS 204 6ASN 102 GLY 203 6 GLU 101 CYS 171 5 ARG 97 ASN 12 5 ASN 102 PHE 223 4ASN 102 LYS 166 4 ARG 97 GLY 211 4 ARG 97 GLN 170 4 GLU 101 ARG 405 3ASN 102 PHE 3 3 GLU 101 GLU 175 2 ARG 97 VAL 220 2 ARG 93 GLY 203 2 LYS94 THR 174 1 LEU 90 LYS 199 1 LEU 116 ASN 180 1 LEU 113 ASP 212 1 LEU113 ASP 202 1 GLY 103 ASN 15 1 GLU 101 THR 7 1 GLU 101 PHE 437 1 GLN 114ASP 202 1 ASN 102 ARG 405 1 ARG 97 TYR 434 1 ARG 97 PRO 182 1 ARG 97 GLY9 1 ARG 97 GLU 8 1 ALA 99 ASP 202 1

Example 5

This example describes the simulations which were run to investigate theinteraction between a) CsgG-Eco-(Y51A/F56Q)-StrepII(C))9 (SEQ ID NO: 2with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus pore mutant No. 25) with T4Dda-(E94C/F98W/C109A/C136A/K194L/A360C) (SEQ ID NO: 24 with mutationsE94C/F98W/C109A/C136A/K194L/A360C and then (ΔM1)G1G2) and b)CsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus pore mutant No. 26) with T4 Dda(E94C/F98W/C109A/C136A/K194L/A360C) (SEQ ID NO: 24 with mutationsE94C/F98W/C109A/C136A/K194L/A360C and then (ΔM1)G1G2).

Simulation Methods

Simulations were performed as described in Example 4.

The CsgG-Eco-(Y51A/F56Q)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus pore mutant No. 25) andCsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus pore mutant No. 26) models were based on the crystalstructures of CsgG found in the protein data bank, accession codes 4UV3and 4Q79. The relevant mutations were made using PyMOL. The resultantpore model was then energy minimised using the steepest descentsalgorithm.

The T4 Dda-(E94C/F98W/C109A/C136A/K194L/A360C) (SEQ ID NO: 24 withmutations E94C/F98W/C109A/C136A/K194L/A360C and then (ΔM1)G1G2) modelwas based on the Dda1993 structure found in the protein data bank,accession code 3UPU. Again, relevant mutations were made using PyMOL,and the model was energy minimised using the steepest descentsalgorithm.

The T4 Dda-(E94C/F98W/C109A/C136A/K194L/A360C) (SEQ ID NO: 24 withmutations E94C/F98W/C109A/C136A/K194L/A360C and then (ΔM1)G1G2) modelwas then placed above mutant pores 25 and 26.

In the simulations the enzyme was oriented such that the 5′ end of theDNA was pointing towards the pore, and the enzyme was unrestrainedthroughout the simulation. For each of the mutant pores investigated twosimulations were run—in the first the pore backbone was restrained andthe simulation box was solvated and in the second the pore backbone wasrestrained except for the cap region and the simulation was boxsolvated. The system was simulated in the NPT ensemble for 40 ns, usingthe Berendsen thermostat and Berendsen barostat to 300 K.

The contacts between the enzyme and pore were analysed using bothGROMACS analysis software and also locally written code. The tablesbelow show the number of contacts observed for both pore and enzymeamino acids (for mutants 25 and 26 with T4Dda-(E94C/F98W/C109A/C136A/K194L/A360C)). Tables 9 (pore backbonerestrained) and 10 (pore backbone restrained with cap regionunrestrained) show the amino acid contact points on pore mutant 25 andthe number of contacts that they make with the enzyme (T4Dda-(E94C/F98W/C109A/C136A/K194L/A360C)). Tables 11 (pore backbonerestrained) and 12 (pore backbone restrained with cap regionunrestrained) show the amino acid contact points on pore mutant 25(CsgG-Eco-(Y51A/F56Q)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) which interact with the amino acid contact points on theenzyme (T4 Dda-(E94C/F98W/C109A/C136A/K194L/A360C)). Tables 13 (porebackbone restrained) and 14 (pore backbone restrained with cap regionunrestrained) show the amino acid contact points on pore mutant 26 andthe number of contacts that they make with the enzyme (T4Dda-(E94C/F98W/C109A/C136A/K194L/A360C)). Tables 15 (pore backbonerestrained) and 16 (pore backbone restrained with cap regionunrestrained) show the amino acid contact points on pore mutant 26(CsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)) which interact with the amino acid contact points on theenzyme (T4 Dda-(E94C/F98W/C109A/C136A/K194L/A360C)). FIG. 33 shows aninitial snapshot of pore mutant 26 and T4Dda-(E94C/F98W/C109A/C136A/K194L/A360C).

TABLE 9 Number of Amino Acid Position Contacts GLU 101 26081 ARG 9712985 GLN 100 6485 ASN 102 4941 LEU 113 3923 LYS 94 3159 ARG 110 2348GLN 114 617 ILE 111 195 ALA 98 74 ILE 107 67 THR 104 24 PRO 112 21 SER115 17 GLY 103 17 GLN 87 13 LEU 90 6 ASN 108 3

TABLE 10 Number of Amino Acid Position Contacts ARG 97 17462 GLU 10112262 ASN 102 9008 LYS 94 5982 GLN 100 3471 GLY 103 3366 LEU 113 1511GLN 87 734 THR 104 500 ARG 110 420 ASN 91 273 GLN 114 178 ALA 98 94 ARG93 44 ILE 111 21 PRO 112 13 LEU 90 13 SER 115 4 VAL 105 2 ALA 99 2 ILE95 1

TABLE 11 Pore Enzyme Amino Acid Position Amino Acid Position Number ofContacts GLU 101 TYR 318 7116 GLU 101 THR 210 6306 GLN 100 ASN 365 4693GLU 101 TRP 195 4608 LEU 113 ASN 367 3910 LYS 94 ASP 212 2369 ASN 102LYS 371 2088 GLU 101 LYS 364 1903 ARG 97 SER 224 1883 ARG 97 TYR 4381764 ARG 110 LYS 368 1727 GLU 101 LYS 358 1443 GLN 100 ASN 367 1390 GLU101 GLN 422 1356 ARG 97 TRP 195 1318 ARG 97 PHE 209 1095 ARG 97 TYR 318965 ARG 97 TYR 350 895 ASN 102 LYS 358 833 ARG 97 GLU 361 818 ARG 97 GLY208 706 GLU 101 GLY 316 697 GLU 101 GLU 317 678 ARG 97 GLU 317 647 GLN114 ASN 367 617 GLU 101 LYS 371 506 ASN 102 TRP 366 466 ARG 97 THR 210463 ASN 102 ARG 207 457 LYS 94 ASP 217 423 GLU 101 ARG 207 409 ASN 102GLU 419 405 GLN 100 LYS 368 402 GLU 101 ARG 321 354 ARG 110 GLY 369 332ARG 97 GLN 422 324 ASN 102 GLY 313 313 ARG 97 ASN 221 306 ARG 97 VAL 439301 ARG 110 ASN 365 274 SER 257 GLU 258 267 GLU 101 LYS 310 217 ILE 111ASN 367 195 ARG 97 ASP 198 154 GLU 101 SER 224 154 ARG 97 VAL 418 145ARG 97 ALA 157 137 GLU 101 GLY 208 136 ARG 97 GLU 419 135 LYS 94 TYR 415111 ARG 97 VAL 220 105 ASN 102 PRO 315 104 ASN 102 GLU 93 103 ARG 97 LYS364 97 LYS 94 TYR 350 94 ARG 97 GLU 154 92 ARG 97 ALA 416 82 GLU 101 PHE223 76 ILE 107 LYS 368 67 ARG 97 GLU 347 66 ARG 97 TYR 415 60 ASN 102TYR 197 57 LYS 94 GLY 211 49 LYS 94 THR 213 47 GLU 101 ASN 365 46 ARG 97LEU 354 41 LYS 94 ARG 216 41 ALA 98 TRP 195 37 ASN 102 TRP 195 34 ALA 98LYS 358 32 ASN 102 LEU 194 27 THR 104 TRP 366 24 ARG 97 GLY 211 23 PRO112 ASN 367 21 GLU 101 PHE 209 21 ASN 102 LYS 364 20 LYS 94 ALA 416 19SER 115 TRP 366 17 GLY 103 LEU 194 17 ARG 97 ASP 212 16 GLU 101 TYR 41515 ARG 110 GLY 370 15 ARG 97 LYS 351 14 ASN 102 LYS 310 14 ASN 102 GLU154 14 ARG 97 CYS 360 13 ARG 97 THR 156 12 GLU 101 LEU 194 11 GLN 87 ASP212 9 ARG 97 PHE 308 8 GLU 101 LEU 354 8 LEU 113 TRP 366 7 ARG 97 ARG321 7 GLU 101 ALA 157 7 LEU 113 ASN 365 6 GLU 101 GLY 193 6 ARG 97 ASP217 5 ALA 98 THR 210 5 GLN 87 ARG 216 4 ARG 97 LEU 319 4 ARG 97 ASN 1554 LYS 94 VAL 220 4 LEU 90 TYR 415 3 LEU 90 ASP 212 3 ARG 97 PHE 223 3ARG 97 GLY 193 3 ARG 97 ALA 421 3 ASN 108 LYS 368 3 ASN 102 GLY 316 3GLU 101 VAL 418 3 ARG 97 ILE 159 2 GLU 101 PRO 315 2 SER 257 ASP 260 1ARG 97 GLY 357 1 ASN 102 THR 210 1 ASN 102 ILE 196 1 ASN 102 GLU 317 1GLU 101 LYS 227 1 GLU 101 GLU 361 1 GLU 101 ASN 221 1 LYS 94 VAL 418 1LYS 94 GLU 154 1

TABLE 12 Pore Enzyme Amino Acid Position Amino Acid Position Number ofContacts ARG 97 ASN 365 3386 GLU 101 GLY 316 2967 GLY 103 ASP 189 2773LYS 94 ASP 212 2524 GLU 101 GLU 317 2401 ASN 102 TYR 197 2377 GLN 100ASN 365 2241 GLU 101 LYS 358 2110 ARG 97 GLU 317 2031 GLU 101 THR 2102025 ASN 102 ASP 189 1985 LYS 94 THR 213 1689 LEU 113 ASN 367 1509 ARG97 GLU 361 1421 ARG 97 TRP 195 1361 ARG 97 TYR 438 1315 ARG 97 VAL 4391145 LYS 94 ASP 217 957 GLU 101 TYR 318 852 GLU 101 ASN 365 797 SER 257ASP 260 784 ARG 97 GLY 193 744 ARG 97 GLU 419 738 ARG 97 PHE 209 731 ASN102 ARG 321 719 ASN 102 TRP 195 708 ASN 102 LYS 371 686 ARG 97 GLN 422637 GLN 87 ASP 212 603 ARG 97 TYR 318 603 ARG 97 ASN 367 575 ARG 97 ASP198 543 GLN 100 ASN 367 517 LYS 94 TYR 350 470 ARG 97 ALA 157 446 ARG 97GLY 208 444 SER 257 GLU 258 425 GLU 101 LYS 371 407 GLU 101 LYS 364 400ASN 102 GLU 93 389 GLN 100 LYS 368 383 ARG 110 LYS 368 357 ARG 97 THR210 303 ASN 91 ARG 216 273 THR 104 ASN 367 214 GLY 103 TYR 197 204 GLN114 ASN 367 178 GLU 101 ARG 207 173 ASN 102 TRP 366 171 ASN 102 GLY 369153 ASN 102 LEU 194 123 ASN 102 GLY 313 120 ARG 97 THR 362 100 THR 104TRP 366 99 GLY 103 THR 164 97 LYS 94 TRP 195 94 GLN 100 GLY 193 84 GLY103 LYS 177 81 ASN 102 LYS 166 80 ARG 97 ILE 159 78 LYS 94 ALA 416 76GLN 87 ARG 216 75 ASN 102 SER 306 73 ASN 102 ARG 207 73 ALA 98 TRP 19568 ARG 97 TYR 158 65 ASN 102 GLU 347 65 ASN 102 GLN 170 65 SER 257 LYS261 62 ARG 97 ASN 192 62 GLN 100 GLY 369 61 THR 104 LYS 199 60 ARG 97LEU 194 57 ASN 102 PHE 163 54 ASN 102 GLU 348 53 GLY 103 GLY 313 53 GLN100 GLU 419 53 ASN 102 LYS 351 52 GLN 87 THR 213 51 LYS 94 GLY 211 49GLN 100 GLN 423 49 THR 104 LYS 166 48 GLU 101 ARG 321 45 ARG 97 PHE 30844 ARG 93 GLU 419 44 ASN 102 GLY 370 41 ARG 110 GLY 369 41 SER 257 THR259 40 ARG 97 GLY 211 40 ARG 97 THR 156 39 ASN 102 THR 164 39 LYS 94 ARG216 39 ARG 97 ARG 321 38 GLY 103 LYS 166 35 ASN 102 GLY 208 33 GLU 101GLY 370 30 LYS 94 GLU 361 28 ASN 102 SER 224 27 GLU 101 ILE 159 25 THR104 PHE 308 23 THR 104 ASN 365 21 ASN 102 PRO 315 21 LYS 94 GLU 154 21ILE 111 ASN 367 21 ARG 110 ILE 159 20 GLY 103 ARG 321 20 GLN 100 LEU 19420 ARG 97 GLU 347 18 ARG 97 ARG 122 16 GLY 103 TRP 366 16 GLY 103 GLY369 15 PRO 112 ASN 367 13 ALA 98 ARG 216 13 ARG 97 SER 345 12 ASN 102LYS 364 12 GLN 100 GLY 370 12 GLU 101 PRO 315 11 GLN 100 ILE 159 11 GLN100 GLU 317 11 LEU 90 VAL 418 10 ASN 102 VAL 220 10 ASN 102 LYS 255 10ALA 98 LYS 358 10 THR 104 ASN 180 9 GLY 103 LEU 194 9 THR 104 LYS 368 8LYS 94 TYR 415 8 GLN 100 THR 164 8 ARG 97 VAL 418 7 ARG 97 VAL 220 7 ARG97 TRP 366 7 ASN 102 LEU 319 7 GLY 103 LYS 255 7 LYS 94 ILE 413 7 GLN100 PHE 163 7 THR 104 LYS 255 6 THR 104 LYS 177 6 LYS 94 GLU 347 6 GLN100 ASN 192 6 GLN 87 ALA 416 5 ARG 97 LYS 368 5 ARG 97 ASP 217 5 ASN 102ARG 216 5 LYS 94 VAL 439 5 ASN 102 VAL 200 4 ASN 102 ASN 365 4 GLU 101LYS 310 4 GLU 101 GLY 313 4 GLY 103 PHE 223 4 LYS 94 ASN 155 4 GLN 100LEU 420 4 ARG 97 SER 224 3 ARG 97 ASP 417 3 ASN 102 THR 362 3 SER 115GLU 419 3 GLU 101 LEU 194 3 GLU 101 GLY 369 3 GLY 103 ASN 192 3 LYS 94ASP 417 3 VAL 105 LYS 166 2 LEU 113 ASN 365 2 LEU 90 ASP 212 2 ARG 97TYR 92 2 ARG 97 GLU 154 2 ARG 97 ARG 207 2 THR 104 TYR 197 2 THR 104 ASP185 2 ASN 102 PHE 209 2 ASN 102 ILE 159 2 GLY 103 PHE 308 2 GLY 103 LEU319 2 GLY 103 ILE 159 2 ALA 98 THR 210 2 ALA 99 ILE 159 2 GLN 100 THR210 2 SER 257 LYS 254 1 ILE 95 ARG 216 1 LEU 90 THR 213 1 ARG 97 TYR 3041 ARG 97 ASP 212 1 THR 104 GLY 369 1 THR 104 ASN 192 1 ASN 102 VAL 314 1ASN 102 THR 210 1 ASN 102 PHE 223 1 ASN 102 LYS 199 1 SER 115 ASP 212 1ARG 110 GLU 317 1 ARG 110 ASN 365 1 GLY 103 PRO 315 1 GLY 103 ASN 367 1ALA 98 ALA 157 1 LYS 94 VAL 418 1

TABLE 13 Number of Amino Acid Position Contacts GLU 101 18418 TRP 9712195 ASN 102 5232 GLY 103 212 ALA 98 113 SER 115 89 THR 104 57 LYS 9452 LEU 113 11 GLN 100 5 ARG 110 5 GLN 114 4 ARG 93 1

TABLE 14 Number of Amino Acid Position Contacts TRP 97 16770 ASN 10211609 GLU 101 4947 GLY 103 2211 THR 104 2187 GLN 100 1589 LYS 94 686 ALA98 289 SER 115 274 ARG 110 251 ARG 93 44 ILE 95 14 LEU 113 5 ASN 91 5LEU 116 4 VAL 105 1 LEU 90 1

TABLE 15 Pore Enzyme Amino Amino Number of Acid Position Acid PositionContacts GLU 101 TRP 195 5230 TRP 97 GLY 211 4360 GLU 101 THR 210 3265GLU 101 LYS 358 3046 GLU 101 GLN 422 2476 ASN 102 ASP 212 1980 TRP 97ARG 216 1707 TRP 97 ASN 365 1445 TRP 97 GLU 361 944 GLU 101 LYS 368 937TRP 97 GLU 419 909 GLU 101 ALA 157 906 ASN 102 LYS 368 842 GLU 101 TYR318 764 TRP 97 THR 210 720 ASN 102 TRP 366 626 GLU 101 ARG 216 518 TRP97 ASN 155 487 GLU 101 LYS 364 482 ASN 102 GLU 361 409 ASN 102 THR 210292 GLU 101 ASN 365 284 GLU 101 GLY 211 261 TRP 97 TRP 366 253 ASN 102TRP 195 243 ASN 102 ASN 365 239 TRP 97 GLN 422 230 TRP 97 VAL 418 205ASN 102 LYS 358 204 TRP 97 THR 156 195 GLY 103 GLY 193 152 TRP 97 GLU154 148 ASN 102 THR 213 129 TRP 97 ASP 212 128 ALA 98 ASP 212 112 TRP 97THR 213 112 TRP 97 ALA 157 101 SER 115 ASP 212 76 ASN 102 LEU 194 75 GLU101 PRO 315 61 ASN 102 VAL 314 59 THR 104 TRP 366 56 TRP 97 TYR 350 48GLU 101 GLY 193 46 TRP 97 LYS 364 45 ASN 102 PRO 315 45 GLU 101 THR 15638 ASN 102 GLU 317 37 GLU 101 LEU 194 36 TRP 97 PHE 209 32 GLY 103 LEU194 31 TRP 97 TYR 318 30 LYS 94 GLU 154 30 TRP 97 GLY 193 28 TRP 97 ALA214 27 GLU 101 GLU 317 25 ASN 102 GLU 154 22 TRP 97 LEU 354 18 GLY 103TRP 366 14 ALA 115 TRP 366 13 TRP 97 ASP 417 12 LEU 113 TRP 366 11 GLU101 VAL 418 11 ASN 102 GLY 211 10 GLU 101 ARG 207 10 GLY 103 LYS 368 9GLU 101 VAL 314 8 LYS 94 VAL 418 8 ASN 102 LYS 166 7 GLU 101 LYS 166 7GLY 103 ASN 365 6 TRP 97 LYS 358 5 ASN 102 LYS 364 5 ARG 110 ASN 365 5LYS 94 TYR 350 5 GLN 114 TRP 366 4 LYS 94 ASN 155 4 GLN 100 ASN 365 4ASN 102 GLY 313 3 GLU 101 ASP 212 3 LYS 94 ALA 416 3 ASN 102 GLY 316 2ASN 102 ALA 157 2 GLU 101 LYS 126 2 ALA 98 GLY 211 1 TRP 97 VAL 439 1TRP 97 VAL 314 1 TRP 97 TRP 195 1 TRP 97 GLU 347 1 TRP 97 GLU 317 1 TRP97 ARG 122 1 THR 104 LYS 368 1 ARG 93 TRP 366 1 ASN 102 THR 362 1 GLU101 CYS 360 1 GLU 101 ARG 321 1 LYS 94 HIS 414 1 LYS 94 ASP 417 1 GLN100 LYS 368 1

TABLE 16 Pore Enzyme Number of Amino Acid Position Amino Acid PositionContacts TRP 97 GLU 361 3862 TRP 97 GLU 317 3269 TRP 97 GLU 154 2166 ASN102 GLY 313 2086 ASN 102 THR 210 2009 GLU 101 TRP 195 1896 ASN 102 ASN365 1656 THR 104 GLU 419 1510 TRP 97 ASN 365 1488 TRP 97 ARG 216 1435GLN 100 ALA 157 1204 GLY 103 TRP 195 1191 GLU 101 ASN 365 1106 GLU 101LYS 368 1100 ASN 102 TRP 195 822 SER 257 ASP 260 779 ASN 102 GLU 361 738TRP 97 TRP 195 719 TRP 97 ASN 155 591 ASN 102 ARG 207 535 ASN 102 TRP366 524 GLY 103 LYS 364 514 GLU 101 THR 210 402 TRP 97 THR 210 377 ASN102 GLY 208 371 TRP 97 TYR 318 365 TRP 97 GLN 422 333 TRP 97 PRO 315 316TRP 97 VAL 220 309 THR 104 LYS 368 307 TRP 97 THR 156 304 ASN 102 ALA157 274 SER 115 ASP 212 274 TRP 97 GLY 316 266 GLU 101 GLN 422 264 GLY103 TYR 197 214 ASN 102 ARG 148 203 ASN 102 LYS 368 199 ASN 102 ASP 198199 ASN 102 LYS 255 192 ASN 102 PHE 308 180 TRP 97 GLU 419 174 LYS 94GLY 211 174 GLN 100 ASN 155 168 ASN 102 PHE 223 153 TRP 97 LYS 358 152TRP 97 ASP 198 151 ARG 110 GLY 193 148 GLN 100 GLU 419 144 ASN 102 LYS364 139 ALA 98 ALA 157 135 ASN 102 ILE 159 122 ALA 98 TRP 195 113 THR104 TYR 197 113 TRP 97 THR 362 103 GLY 103 GLY 369 103 LYS 94 THR 210103 LYS 94 ASP 212 89 ASN 102 GLU 154 87 ASN 102 ILE 196 84 LYS 94 TYR415 84 THR 104 GLU 154 77 TRP 97 GLY 193 75 ASN 102 ARG 321 71 TRP 97VAL 418 69 GLU 101 TRP 366 69 THR 104 ASP 198 67 THR 104 ALA 157 64 GLY103 GLU 154 60 LYS 94 GLY 153 60 LYS 94 GLU 154 59 TRP 97 TRP 366 58 GLU101 ARG 207 56 ARG 110 LEU 194 52 ASN 102 GLY 369 46 LYS 94 GLU 361 46GLY 103 LYS 368 42 ARG 93 ASP 212 40 ASN 102 GLU 317 39 GLN 100 THR 15634 TRP 97 VAL 314 32 ALA 98 ASP 212 31 GLY 103 ARG 207 31 LYS 94 PHE 20929 TRP 97 GLY 211 28 ASN 102 ARG 312 28 ARG 110 GLY 313 25 TRP 97 ARG321 22 ASN 102 VAL 220 22 TRP 97 ASP 417 18 THR 104 GLY 369 18 ASN 102THR 164 17 LYS 94 ARG 216 17 TRP 97 GLY 153 16 ASN 102 TYR 158 16 GLY103 LEU 194 16 GLU 101 ILE 159 15 GLN 100 PRO 315 15 ILE 95 ASP 212 14GLY 103 TRP 366 14 TRP 97 LEU 194 13 GLU 101 ARG 321 13 GLN 100 LYS 36813 ASN 102 GLY 153 11 ARG 110 ASN 192 11 GLN 100 TYR 158 10 ASN 102 LYS145 9 GLU 101 ARG 216 9 ARG 110 PRO 315 8 ALA 98 THR 210 7 ASN 102 GLY211 7 ASN 102 ARG 216 7 ARG 110 LYS 368 7 LYS 94 HIS 414 7 LYS 94 ALA214 7 SER 257 GLU 258 6 TRP 97 LYS 255 6 THR 104 ASP 212 6 LYS 94 ASP417 6 ASN 91 ASP 212 5 TRP 97 THR 213 5 TRP 97 LYS 364 5 THR 104 TRP 1955 THR 104 PHE 308 5 GLY 103 LYS 255 5 GLY 103 GLU 419 5 GLY 103 ARG 3215 LEU 116 ASP 212 4 THR 104 TYR 438 4 THR 104 THR 210 4 THR 104 ILE 1594 ARG 93 ARG 216 4 GLU 101 ALA 157 4 GLY 103 ILE 159 4 GLY 103 ASP 198 4LYS 94 ASN 155 4 LEU 113 ARG 216 3 ASN 102 LEU 319 3 GLU 101 VAL 314 3GLU 101 GLY 193 3 LEU 113 TRP 366 2 ASN 102 VAL 314 2 ASN 102 TYR 197 2ASN 102 PHE 209 2 ASN 102 LEU 194 2 GLU 101 THR 362 2 GLU 101 GLY 313 2GLY 103 ILE 196 2 ALA 98 PRO 315 1 ALA 98 GLY 211 1 ALA 98 ASN 155 1 VAL105 LYS 368 1 LEU 90 ASP 212 1 TRP 97 PHE 223 1 TRP 97 PHE 209 1 TRP 97ASP 217 1 TRP 97 ASP 212 1 THR 104 VAL 200 1 THR 104 GLY 370 1 THR 104ARG 207 1 ASN 102 PRO 152 1 ASN 102 LYS 310 1 ASN 102 LYS 227 1 ASN 102GLU 419 1 ASN 102 ARG 122 1 ASN 102 ALA 311 1 GLU 101 VAL 418 1 GLU 101PHE 308 1 GLU 101 LEU 194 1 GLY 103 PHE 308 1 LYS 94 VAL 439 1 GLN 100ARG 122 1

Example 6

This Example describes the characterisation of several CsgG mutantswhich show improved characterisation accuracy.

Materials and Methods

The materials and methods that were used in this example are the same asthose described above for example 2. The enzyme used to control movementwas either Enzyme 1=T4 Dda-E94C/C109A/C136A/A360C (SEQ ID NO: 24 withmutations E94C/C109A/C136A/A360C) or Enzyme 2=T4Dda-E94C/F98W/C109A/C136A/K194L/A360C (SEQ ID NO: 24 with mutationsE94C/F98W/C109A/C136A/K194L/A360C).

The 1D accuracy characterisation measurements were calculated usingmethods as disclosed in the International Application PCT/GB2012/052343(published as WO/2013/041878).

Results

The 1D basecall characterisation accuracy for MspA mutantx=MspA-((Del-L74/G75/D118/L119)D56F/E59R/L88N/D90N/D91N/Q126R/D134R/E139K)8(SEQ ID NO: 50 with mutations D56F/E59R/L88N/D90N/D91N/Q126R/D134R/E139Kand deletion of the amino acids L74/G75/D118/L119) with DNAtranslocation controlled by T4 Dda-E94C/F98W/C109A/C136A/K194L/A360C was68.7%. All of the mutants tested (see Table 17 below) showed improved 1Dbasecall characterisation accuracy in comparison to MspA mutant X.

27—CsgG-Eco-(Y51A/F56Q/R97W/R192Q-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/R97W/R192Q where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)28—CsgG-Eco-(Y51A/F56Q/R97W/R192D-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/R97W/R192D where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)29—CsgG-Eco-(Y51A/F56Q/K135L/T150I/S208V-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/K135L/T150I/S208V where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus)30—CsgG-Eco-(Y51A/F56Q/T150I/S208V-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/T150I/S208V where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)31—CsgG-Eco-(Y51A/F56Q/S208V-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/S208V where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)32—CsgG-Eco-(Y51A/F56Q/T150I-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/T150I where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)33—CsgG-Eco-(Y51A/F56Q/K135V/T150Y-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/K135V/T150Y where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)34—CsgG-Eco-(Y51A/F56Q/K135L-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/K135L where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)35—CsgG-Eco-(Y51A/F56Q/R97F/R192D-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/R97F/R192D where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)36—CsgG-Eco-(Y51A/F56Q/K135L/T150I-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/K135L/T150I where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)37—CsgG-Eco-((Del-D195/Y196/Q197/R198/L199)-Y51A/F56Q-StrepII(C))9 (SEQID NO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47 andis attached at the C-terminus and deletion of the amino acidsD195/Y196/Q197/R198/L199)38—CsgG-Eco-((Del-R192/F193/I194/D195/Y196/Q197/R198/L199/L200)-Y51A/F56Q-StrepII(C))9(SEQ ID NO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus and deletion of the amino acidsR192/F193/I194/D195/Y196/Q197/R198/L199/L200)39—CsgG-Eco-((Del-Q197/R198/L199/L200)-Y51A/F56Q-StrepII(C))9 (SEQ IDNO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus and deletion of the amino acidsQ197/R198/L199/L200)40—CsgG-Eco-((Del-I194/D195/Y196/Q197/R198/L199)-Y51A/F56Q-StrepII(C))9(SEQ ID NO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus and deletion of the amino acidsI194/D195/Y196/Q197/R198/L199)41—CsgG-Eco-((Del-V139/G140/D149/T150/V186/Q187/V204/G205)-Y51A/F56Q-StrepII(C))9(SEQ ID NO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus and deletion of the amino acidsV139/G140/D149/T150/V186/Q187/V204/G205)42—CsgG-Eco-((Del-D195/Y196/Q197/R198/L199/L200)-Y51A/F56Q-StrepII(C))9(SEQ ID NO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus and deletion of the amino acidsD195/Y196/Q197/R198/L199/L200)43—CsgG-Eco-((Del-Y196/Q197/R198/L199/L200/E201)-Y51A/F56Q-StrepII(C))9(SEQ ID NO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus and deletion of the amino acidsY196/Q197/R198/L199/L200/E201)44—CsgG-Eco-((Del-Q197/R198/L199)-Y51A/F56Q-StrepII(C))9 (SEQ ID NO: 2with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus and deletion of the amino acidsQ197/R198/L199)45—CsgG-Eco-((Del-F193/I194/D195/Y196/Q197/R198/L199)-Y51A/F56Q-StrepII(C))9(SEQ ID NO: 2 with mutations Y51A/F56Q where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus and deletion of the amino acidsF193/I194/D195/Y196/Q197/R198/L199)46—CsgG-Eco-(Y51A/F56Q/R192T-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R192T where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)47—CsgG-Eco-(Y51A/F56Q/N102S-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/N102S where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)48—CsgG-Eco-(Y51A/F56Q/Q42R-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/Q42R where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)49—CsgG-Eco-(Y51A/F56Q/R192S-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R192S where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)50—CsgG-Eco-(Y51A/F56Q/G103N-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/G103N where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)51—CsgG-Eco-(Y51A/F56Q/R97N/N102R-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/R97N/N102R where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)52—CsgG-Eco-(Y51A/F56Q/R97L-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97L where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)53—CsgG-Eco-(Y51A/F56Q/R192D-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R192D where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)54—CsgG-Eco-(Y51A/F56Q/R97N/N102G-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/R97N/N102G where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus)55—CsgG-Eco-(Y51A/F56Q/F48S-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/F48S where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)56—CsgG-Eco-(Y51A/F56Q/G103S-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/G103S where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)57—CsgG-Eco-(Y51A/F56Q/E101L-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/E101L where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)58—CsgG-Eco-(Y51A/F56Q/R192Q-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R192Q where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)59—CsgG-Eco-(Y51A/F56Q/K135N/R142N/R192N-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/K135N/R142N/R192N where StrepII(C) is SEQ ID NO: 47and is attached at the C-terminus)60—CsgG-Eco-(Y51A/F56Q/R97N-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97N where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)61—CsgG-Eco-(Y51A/F56Q/R192N-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R192N where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)62—CsgG-Eco-(Y51A/F56Q/Y130W-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/Y130W where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)63—CsgG-Eco-(Y51A/F56Q/E101G-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/E101G where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus)

TABLE 17 1D Basecall Characterisation CsgC Mutant No. Enzyme Accuracy(%) 25 2 72.6 26 2 79.2 27 2 81.3 28 2 80.2 29 2 72.2 30 2 74.7 31 274.5 32 2 73.3 33 2 73.8 34 2 74.3 35 2 75.5 36 2 73.5 37 2 73.4 38 275.3 39 2 72.0 40 2 74.5 41 2 74.8 42 2 71.0 43 2 70.9 44 2 71.9 45 273.0 46 1 75.0 47 1 72.1 48 1 75.0 49 1 74.8 50 1 75.2 51 1 73.1 52 175.4 53 1 77.1 54 1 75.9 55 1 73.7 56 1 73.1 57 1 73.2 58 1 76.8 59 172.7 60 1 76.1 61 1 75.0 62 1 74.7 63 1 73.1 25 1 74.8 26 1 77.4

Example 7

This example compares DNA capture of a number of different mutantnanopores.

Materials and Methods

Electrical measurements were acquired from a variety of single CsgG orMspA nanopores inserted in block co-polymer in buffer (25 mM K Phosphatebuffer, 150 mM Potassium Ferrocyanide (II), 150 mM PotassiumFerricyanide (III), pH 8.0). After achieving a single pore inserted inthe block co-polymer, then buffer (2 mL, 25 mM K Phosphate buffer, 150mM Potassium Ferrocyanide (II), 150 mM Potassium Ferricyanide (III), pH8.0) was flowed through the system to remove any excess nanopores. 150uL of 500 mM KCl, 25 mM K Phosphate, 1.5 mM MgCl2, 1.5 mM ATP, pH8.0 wasthen flowed through the system. After 10 minutes a 150 uL of DNA (SEQ IDNO: 51, 200 nM) was then flowed into the single nanopore experimentalsystem. The experiment was run at −120 mV and helicase-controlled DNAmovement monitored.

Results

The CsgG mutant CsgG-Eco-(Y51A/F56Q/R97W/E101S/R192D-StrepII(C))9 (SEQID NO: 2 with mutations Y51A/F56Q/R97W/E101S/R192D where StrepII(C) isSEQ ID NO: 47 and is attached at the C-terminus) (see FIG. 36) shows ahigher rate of capture (e.g. captures DNA polynucleotides more easily)thanMspA-((Del-L74/G75/D118/L119)D56F/E59R/L88N/D90N/D91N/Q126R/D134R/E139K)8(see FIG. 34). Each spike in the current traces corresponds totranslocation of the DNA polynucleotide (SEQ ID NO: 51) through thenanopore without being controlled by an enzyme. The 10 second currenttraces in FIG. 34 show fewer DNA translocations than the 10 secondcurrent traces for the CsgGnanopore—CsgG-Eco-(Y51A/F56Q/R97W/E101S/R192D-StrepII(C))9.

The mutation of position E101 to E101S resulted in an increase in thecapture rate when compared to a CsgG mutant without the E101S mutation.FIG. 35 shows that the 10 second current traces for CsgG mutantCsgG-Eco-(Y51A/F56Q/R97W/R192D-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W/R192D where StrepII(C) is SEQ ID NO: 47 and is attachedat the C-terminus) exhibited fewer translocations thanCsgG-Eco-(Y51A/F56Q/R97W/E101S/R192D-StrepII(C))9. The average number oftranslocations for CsgG-Eco-(Y51A/F56Q/R97W/R192D-StrepII(C))9 was 7.25per second (n=12) and the average number of translocations forCsgG-Eco-(Y51A/F56Q/R97W/E101S/R192D-StrepII(C))9 was 18 per second(n=14).

Example 8

This example compares the level of expression of two different CsgGmutant pores.

Materials and Methods

The materials and methods that were used to make the nanopores(A=CsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 (SEQ ID NO: 2 with mutationsY51A/F56Q/R97W where StrepII(C) is SEQ ID NO: 47 and is attached at theC-terminus) and B=CsgG-Eco-(Y51A/F56Q/R97W/R192D)-StrepII(C))9 (SEQ IDNO: 2 with mutations Y51A/F56Q/R97W/R192D where StrepII(C) is SEQ ID NO:47 and is attached at the C-terminus)) in this example are the same asthose described above for example 3.

Results

The two nanopores A=CsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9 (SEQ ID NO: 2with mutations Y51A/F56Q/R97W where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus) andB=CsgG-Eco-(Y51A/F56Q/R97W/R192D)-StrepII(C))9 (SEQ ID NO: 2 withmutations Y51A/F56Q/R97W/R192D where StrepII(C) is SEQ ID NO: 47 and isattached at the C-terminus) were expressed and purified using exactlythe same protocol and the same volumes of each nanopore were analysedusing gel filtration chromatograms (120 mL 5200 Column, see FIG. 37) andSDS-PAGE analysis (see FIG. 38). The absorbance value for B (470.3 mAu)was much higher than A (11.4 mAu) which indicated thatCsgG-Eco-(Y51A/F56Q/R97W/R192D)-StrepII(C))9 expressed at a much higherlevel than CsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9. The intensity of thebands in FIG. 38 also indicate the expression level of the two pores.Bands A-C(containing CsgG-Eco-(Y51A/F56Q/R97W)-StrepII(C))9) were lessintense than bands D-E (containingCsgG-Eco-(Y51A/F56Q/R97W/R192D)-StrepII(C))9). The two methods ofanalysis both indicated that the addition of R192D mutation greatlyincreased the observed expression of the CsgG mutant.

Example 9

This Example describes the characterisation of several CsgG mutantswhich show improved characterisation accuracy.

Materials and Methods CsG Pores

The following 8 CsgG mutant pores were tested. Mutant 28 described inExample 9 above was used as the baseline pore. The mutations are made inSEQ ID NO: 2 and the purification tag StrepII has the sequence shown inSEQ ID NO: 47.

Baseline pore (mutant 28): CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9

Mutant A: CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9-del(D195-L199) MutantB: CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9-del(F193-L199) Mutant C:CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9-F191T Mutant D:CsgG-(WT-Y51A/F56Q/R97W/R192D-del(V105I107)-StrepII)9 Mutant E:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105-I107) Mutant F:CsgG-(WT-Y51A/F56Q/R192D-StrepII)9-R93W Mutant G:CsgG-(WT-Y51A/F56Q/R192D-StrepII)9-R93W-del(D195-L199) Mutant H:CsgG-(WT-Y51A/F56Q/R192D-StrepII)9-R93Y/R97Y Nanopore Preparation

To prepare a nanopore array chip that contain multiple wells of blockco-polymer membrane each with a single CsgG mutant nanopore inserted thefollowing method was used. CsgG mutants expressed in E. coli werepurified and stored in buffer containing 25 mM Tris, 150 mM NaCl, 2 mMEDTA, 0.01% DDM, 0.1% SDS, 0.1% Brij 58 at pH8. These mutant CsgG poreswere diluted to 1 in 1 million using buffer comprising 25 mM PotassiumPhosphate, 150 mM Potassium Ferrocyanide (II), 150 mM PotassiumFerricyanide (III) at pH 8.0 and added to chips to obtain single poresin each of the wells. After pore insertion, the array chip was washedwith 1 mL buffer comprising 25 mM Potassium Phosphate, 150 mM PotassiumFerrocyanide (II), 150 mM Potassium Ferricyanide (III) at pH 8.0 toremove excess pores. After a few minutes, each chip was flushed twicewith 500 mL of sequencing mix containing 470 mM KCl, 25 mM HEPES, 11 mMATP and 10 mM MgCl2.

DNA Sample Preparation

DNA sample was prepared for sequencing using the following method. 1 μgof DNA analyte was incubated with the 40 nM of adapter mix containing aT4 Dda helicase enzyme prebound to the adapter and blunt TA ligase for10 minutes (available from https://store.nanoporetech.com/). Thestructure of the adapter is shown in FIG. 43 and the sequences containedin the adapter are set out in SEQ ID NOs: 52 to 55. The ligation mixturewas then purified to remove unligated free adapter using Spripurification. The final ligated mixture was eluted in 25 μL elutionbuffer containing 40 mM CAPS at pH10, 40 mM KCl and 400 nM cholesteroltether. For each chip, 120 of DNA-adpater ligated mix was mixed with thesequencing mix (final volume of 150 μL) and added to chip forsequencing. The experiment was then run for 6 hours at 160 mV.

The 1D accuracy characterisation measurements were calculated usingmethods as disclosed in WO2013/041878.

Measuring Template Speed

The template speed was measured by the following method. The basecall ofeach squiggle was aligned to the reference sequence. The number of basesthat spanned the alignment (alignment end position subtracted from thealignment start position) was divided by the time between the event thatcorresponded to the end of the alignment and by the event thatcorresponded to the start of the alignment.

Results Basecall Accuracy

As shown in FIG. 39, all 8 CsgG mutant pores were found to have animproved basecall accuracy compared to the baseline pore, mutant 28(CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9) described in Example 6. Asshown in Table 17, mutant 28 showed the highest basecall accuracy(80.2%) of all the CsgG mutants tested in Example 6, in which mutant 25(CsgG-(WT-Y51A/F56Q-StrepII)9) described in Example 5 was the baselinemutant. Therefore the deletion of D195-L199, of F193-L199 or V105-I107,or the substitution of F191T results in a further improvement inaccuracy in addition to the improvement in accuracy resulting from theR97W and R192D substitutions in mutant 28.

The deletion of D195-L199, of F193-L199 or V105-I107, or thesubstitution of F191T, would each also be expected to improve accuracyin the presence of other mutations in the CsgG sequence or in theabsence of the R97W, R192D, Y51A and/or F56Q mutations. For example,mutant E, which contains the mutation K94Q in addition to thedel(V105-I107) mutation has an improved accuracy compared to mutant 28,as does the del(V105-I107)-containing mutant G which does not containthe R97W substitution, but instead contains a R93W substitution.

Table 17 in Example 26 shows that mutant 26, which contains the R97Wsubstitution has almost as good a basecall accuracy (79.2%) as mutant 28(80.2%). This suggests that the R97W mutation underlies the increasedbasecall accuracy. In this Example, two mutants which do not contain theR97W mutation (and also do not contain the R192D mutation), but insteadcontain a R93W substitution (mutant F) or both a R93Y substitution and aR97Y substitution (mutant H) were tested and found to have a higherbasecall accuracy than mutant 28. This shows that R93W and R93Y/R97Ysubstitutions can be used to improve the basecall accuracy of CsgGnanopores.

Template Speed and Template Accuracy

As shown in FIG. 40A, mutant D(CsgG-(WT-Y51A/F56Q/R97W/R192D-del(V105-I107)-StrepII)9) has a tighteneddistribution of speed population as compared to the baseline mutant 28CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9.

FIG. 40B shows that mutant D(CsgG-(WT-Y51A/F56Q/R97W/R192D-del(V105-I107)-StrepII)9) has tighteneddistribution of template accuracy as compared to the baseline mutant 28CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9.

It is an advantage to have a tightened speed and accuracy distributionsince there is less variation in the data. Also, the median accuracy ofthe data will increase by reducing the amount of lower accuracy datagenerated. Thus, deleting the amino acids from V105 to I107 of a CsgGnanopore can be used to produce a CsgG nanopore with improved propertiesfor characterising polynucleotides.

Example 10

This Example describes the characterisation of CsgG mutants which show areduction in noisy pore signal.

Materials and Methods CsG Pores

The following CsgG mutant pores were tested. Mutant 28 described inExample 9 above was used as the baseline pore. The mutations are made inSEQ ID NO: 2 and the purification tag StrepII has the sequence shown inSEQ ID NO: 47.

Baseline pore (mutant 28): CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9

Mutant I: CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9-K94N. Mutant J:CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9-K94Q. Nanopore Preparation

Chips containing multiple wells of block co-polymer membrane each with asingle CsgG mutant nanopore inserted were prepared as described inExample 9.

DNA Sample Preparation

DNA sample was prepared for sequencing using the method described inExample 9.

Determining Time Spent in Noisy Pore State

The percentage of time spent in a noisy pore state was calculated asfollows. The event detected signal within each channel was split up intonon-overlapping short windows. For each window the mean average of thecurrent levels and the dispersion of the current levels was calculated.The values obtained were then passed to a classifier which returned alabel denoting whether the window contained a noisy signal. Theclassifier was trained to detect noisy signals by providing it withpre-labelled data.

Results Noisy Pore State

FIG. 41 displays an example “squiggle” that shows the “noisy” pore errormode exhibited by baseline mutant 28CsgG-(WT-Y51A/F56Q/R97W/R192D-StrepII)9. The top panel of FIG. 41 showsthe difference in flow of current through the pore during the “good” and“noisy” pore states. The bottom panel of FIG. 41 shows an expanded viewof the transition from “good” state to “noisy” state.

FIG. 42 shows the reduction in noisy pore state of mutant pores I and Jwhen compared to baseline mutant 28, averaged over at least 5 runs.

The percentage of time spent in noise pore state by both Mutant J andMutant I is significantly reduced compared to the baseline. Mutants Iand J differ from the mutant 28 used as a baseline at just one residue.Both mutant I and mutant J contain a substitution of K94. Mutant Icontains a K94N mutation and mutant II contains a K94Q mutation.Therefore substitution of K94 in a CsgG nanopore, particularlysubstitution with N or Q, can be used to produce a CsgG nanopore withimproved properties for characterizing polynucleotides.

Example 11

This Example describes the characterisation of several CsgG mutantswhich show increased capture activity.

Materials and Methods CsG Pores

The following CsgG mutant pores were tested. Mutant E described inExample 9 above was used as the baseline pore. The mutations are made inSEQ ID NO: 2 and the purification tag StrepII has the sequence shown inSEQ ID NO: 47.

Baseline (mutant E): CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105-I107).

Mutant K: CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-Q42K MutantL: CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-E44N Mutant M:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-E44Q Mutant N:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-L90R Mutant O:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-N91R Mutant P:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105-I107)-195R Mutant Q:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-A99R Mutant R:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-E101H Mutant S:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-E101K Mutant T:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-E101N Mutant U:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-E101Q Mutant V:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105I107)-E101T Mutant W:CsgG-(WT-Y51A/F56Q/K94Q/R97W/R192D-del(V105-I107)-Q114K NanoporePreparation

To prepare nanopore array chips that contain multiple wells of blockco-polymer membrane each with a single CsgG mutant nanopore inserted thefollowing method was used. CsgG mutants expressed in E. coli werepurified and stored in buffer containing 25 mM Tris, 150 mM NaCl, 2 mMEDTA, 0.01% DDM, 0.1% SDS, 0.1% Brij 58 at pH8. These mutant CsgG poreswere diluted to 1 in 1 million using buffer comprising 25 mM PotassiumPhosphate, 150 mM Potassium Ferrocyanide (II), 150 mM PotassiumFerricyanide (III) at pH 8.0 and added to the chips to obtain singlepores in each of the wells. After pore insertion, the chips were washedwith 1 mL buffer comprising 25 mM Potassium Phosphate, 150 mM PotassiumFerrocyanide (II), 150 mM Potassium Ferricyanide (III) at pH 8.0 toremove excess pores. 1 mL of solution containing 240 nM TBA analyte in25 mM Potassium Phosphate, 150 mM Potassium Ferrocyanide (II), 150 mMPotassium Ferricyanide (III) at pH 8.0 was flushed into the chip.

Determining Capture Ability

The ability of a mutant pore to capture DNA analyte is then assessed byits ability to capture Thrombin Binding Aptamer (TBA) (SEQ ID NO: 51).The experiment was run at 180 mV. In order to measure TBA capture by apore, the median time between TBA events was calculated.

Results

As shown in FIG. 44, the median time between TBA events for 13 mutantswas significantly reduced compared to the baseline, indicating that all13 mutants display increased capture rates of template DNA.

Each of the 13 mutants had a single amino acid substitution compared tothe baseline pore. The particular substitutions were: Q42K, E44N, E44Q,L90R, N91R, I95R, A99R, E101H, E101K, E101N, E101Q, E101T and Q114K. Allof these mutations involve the substitution of a negatively chargedamino acid with an uncharged amino acid or a positively charged aminoacid, or of an uncharged amino acid with a positively charged aminoacid. Therefore, it can be concluded that substitution of the amino acidat one or more of positions Q42, E44, E44, L90, N91, 195, A99, E101 andQ114 with amino acids that remove the negative charge and/or increasethe positive charge at these positions results in increased capture of apolynucleotide.

Sequence Alignment of the Various CsgG Homologues

FIG. 45 shows the sequence alignment between the twenty-one CsgGhomologues as detailed above. A multiple sequence alignment wasperformed on SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQID NO: 6, SEQ ID NO: 7, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34,SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO:39, SEQ ID NO: 40 and SEQ ID NO: 41.

Praline software, a multiple sequence alignment toolbox that integrateshomology-extended and secondary structure information was used toperform the alignment http://www.ibi.vu.nl/programs/pralinewww/, seealso Simossis VA1, Heringa J.; Nucleic Acids Res. 2005 Jul. 1; 33 (WebServer issue):W289-94. The alignment was scored using the BLOSUM62residue exchange matrix. For details of this method, see for exampleHenikoff S, Henikoff J G; Proc. Natl. Acad. Sci. USA Vol. 89, pp.10915-10919, November 1992. Gap opening and extension penalties of 12and 1 were used respectively. Secondary structure prediction usingPSIPRED was used to guide the alignment. For details of this method, seefor example Jones D. T.; J Mol Biol. 1999 Sep. 17; 292(2):195-202. Theabove methods used to align the sequences are exemplary and othermethods of sequence alignment known in the art may be used.

With reference to the sequence alignments of FIG. 45, each section ofsequence alignment the conservation at each position is indicated by ahistogram and a score. Numbers 0-9 on the scale indicate increasingconservation, columns with mutations which result in similar propertiesof that amino being conserved are marked with a plus (′+′) and the starsymbol (″″) indicates 100% sequence identity at that position. It can beseen from the conservation values of the sequence alignment that many ofthe residues show very high or even perfect sequence identity indicatingthat these 21 homologues are closely related.

FIG. 46 shows the same relative sequence alignments as FIG. 45 withpredicted alpha helical secondary structure regions additionally shadedin grey. FIG. 47 shows the same relative sequence alignments as FIG. 45with predicted beta sheet secondary structure regions additionallyshaded in grey. FIGS. 46 and 47 show that the regions of predicted alphahelices and beta sheets of these homologues, important secondarystructures for CsgG nanopores are highly conserved.

The multiple sequence alignment strongly suggests the sequences arerelated; not only is there a high degree of conservation along thealignment, but the predicted secondary structural elements are alsoaligned.

The sequence alignments in FIGS. 45, 46 and 47 may be used as areference to show the relative positions that align with each other.Thus amino-acid residues identified with respect to SEQ ID NO 2 and thecorresponding amino-acid residues in other CsgG homologues can beidentified. For ease of identification, residues R97 and R192 have beenlocated with an asterisk. It can be seen from the table that for exampleR192 of SEQ ID NO: 2 corresponds to residue R191 of SEQ ID NO: 32 andresidue K177 of SEQ ID NO: 37.

As will be readily appreciated with reference to FIGS. 45 to 47, theCsgG monomers are highly conserved. Furthermore, from knowledge of themutations in relation to SEQ ID NO: 2 it is possible to determine theequivalent positions for mutations of CsgG monomers other than that ofSEQ ID NO: 2.

Thus reference to a mutant CsgG monomer comprising a variant of thesequence as shown in SEQ ID NO: 2 and specific amino-acid mutationsthereof as set out in the claims and elsewhere in the specification alsoencompasses a mutant CsgG monomer comprising a variant of the sequenceas shown in SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQID NO: 7, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30,SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO:35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ IDNO: 40 and SEQ ID NO: 41 and corresponding amino-acid mutations thereof.Likewise reference to a construct, pore or method involving the use of apore relating to a mutant CsgG monomer comprising a variant of thesequence as shown in SEQ ID NO: 2 and specific amino-acid mutationsthereof as set out in the claims and elsewhere in the specification alsoencompasses a construct, pore or method relating to a mutant CsgGmonomer comprising a variant of the sequence according the abovedisclosed SEQ ID NOS and corresponding amino-acid mutations thereof. Ifwill further be appreciated that the invention extends to other variantCsgG monomers not expressly identified in the specification that showhighly conserved regions.

1. A mutant CsgG monomer comprising a variant of the sequence shown inSEQ ID NO: 2 which comprises R192D/Q/F/S/T.
 2. A mutant CsgG monomeraccording to claim 1, wherein the variant comprises R192D.
 3. A mutantCsgG monomer according to claim 1, wherein the variant comprises (a) oneor more mutations at the following positions (i.e. mutations at one ormore of the following positions) I41, R93, A98, Q100, G103, T104, A106,I107, N108, L113, S115, T117, Y130, K135, E170, S208, D233, D238 andE244 and/or (b) one or more of D43S, E44S, F48S/N/Q/Y/W/I/V/H/R/K,Q87N/R/K, N91K/R, K94R/F/Y/W/L/S/N, R97F/Y/W/V/I/K/S/Q/H, E101I/L/A/H,N102K/Q/L/I/V/S/H, R110F/G/N, Q114R/K, R142Q/S, T150Y/A/V/L/S/Q/N andD248S/N/Q/K/R; (A) deletion of one or more positions F193, I194, D195,Y196, Q197, R198, L199, L200 and E201 and/or (B) deletion of one or moreof V139/G140/D149/T150/V186/Q187/V204/G205,G137/G138/Q151/Y152/Y184/E185/Y206/T207 andA141/R142/G147/A148/A188/G189/G202/E203; and/or one or more of thefollowing: (i) one or more mutations at the following positions N40,D43, E44, S54, S57, Q62, R97, E101, E124, E131, R142 and T150; (ii)mutations at Y51/N55, Y51/F56, N55/F56 or Y51/N55/F56; (iii) Q42R orQ42K; (iv) K49R or K49Q; (v) N102R, N102F, N102Y or N102W; (vi) D149N,D149Q or D149R; (vii) E185N, E185Q or E185R; (viii) D195N, D195Q orD195R; (ix) E201N, E201Q or E201R; (x) E203N, E203Q or E203R; (xi)deletion of one or more of the following positions F48, K49, P50, Y51,P52, A53, S54, N55, F56 and S57; (xii) one or more mutations at thefollowing positions L90, N91, I95, A99, Q114; and (xiii) R97W; R93W;R93Y and R97Y; F191T; deletion of V105, A106 and I107; and/or deletionof F193, I194, D195, Y196, Q197, R198 and L199 or deletion of D195,Y196, Q197, R198 and L199.
 4. A mutant monomer according to claim 1,wherein the variant comprises a mutation at Y51 and/or F56.
 5. A mutantmonomer according to claim 4, wherein the mutation at Y51 is Y51A and/orthe mutation at F56 is F56Q.
 6. A mutant monomer according to claim 1,wherein (a) the variant comprises one or more of the followingsubstitutions N40R, N40K, D43N, D43Q, D43R, D43K, E44N, E44Q, E44R,E44K, S54P, S57P, Q62R, Q62K, R97N, R97G, R97L, E101N, E101Q, E101R,E101K, E101F, E101Y, E101W, E101T, E124N, E124Q, E124R, E124K, E124F,E124Y, E124W, E131D, R142E, R142N and T150I; (b) the variant comprisesF56N/N55Q, F56N/N55R, F56N/N55K, F56N/N55S, F56N/N55G, F56N/N55A,F56N/N55T, F56Q/N55Q, F56Q/N55R, F56Q/N55K, F56Q/N55S, F56Q/N55G,F56Q/N55A, F56Q/N55T, F56R/N55Q, F56R/N55R, F56R/N55K, F56R/N55S,F56R/N55G, F56R/N55A, F56R/N55T, F56S/N55Q, F56S/N55R, F56S/N55K,F56S/N55S, F56S/N55G, F56S/N55A, F56S/N55T, F56G/N55Q, F56G/N55R,F56G/N55K, F56G/N55S, F56G/N55G, F56G/N55A, F56G/N55T, F56A/N55Q,F56A/N55R, F56A/N55K, F56A/N55S, F56A/N55G, F56A/N55A, F56A/N55T,F56K/N55Q, F56K/N55R, F56K/N55K, F56K/N55S, F56K/N55G, F56K/N55A,F56K/N55T, F56N/Y51L, F56N/Y51V, F56N/Y51A, F56N/Y51N, F56N/Y51Q,F56N/Y51S, F56N/Y51G, F56Q/Y51L, F56Q/Y51V, F56Q/Y51A, F56Q/Y51N,F56Q/Y51Q, F56Q/Y51S, F56Q/Y51G, F56R/Y51L, F56R/Y51V, F56R/Y51A,F56R/Y51N, F56R/Y51Q, F56R/Y51S, F56R/Y51G, F56S/Y51L, F56S/Y51V,F56S/Y51A, F56S/Y51N, F56S/Y51Q, F56S/Y51S, F56S/Y51G, F56G/Y51L,F56G/Y51V, F56G/Y51A, F56G/Y51N, F56G/Y51Q, F56G/Y51S, F56G/Y51G,F56A/Y51L, F56A/Y51V, F56A/Y51A, F56A/Y51N, F56A/Y51Q, F56A/Y51S,F56A/Y51G, F56K/Y51L, F56K/Y51V, F56K/Y51A, F56K/Y51N, F56K/Y51Q,F56K/Y51S, F56K/Y51G, N55Q/Y51L, N55Q/Y51V, N55Q/Y51A, N55Q/Y51N,N55Q/Y51Q, N55Q/Y51S, N55Q/Y51G, N55R/Y51L, N55R/Y51V, N55R/Y51A,N55R/Y51N, N55R/Y51Q, N55R/Y51S, N55R/Y51G, N55K/Y51L, N55K/Y51V,N55K/Y51A, N55K/Y51N, N55K/Y51Q, N55K/Y51S, N55K/Y51G, N55S/Y51L,N55S/Y51V, N55S/Y51A, N55S/Y51N, N55S/Y51Q, N55S/Y51S, N55S/Y51G,N55G/Y51L, N55G/Y51V, N55G/Y51A, N55G/Y51N, N55G/Y51Q, N55G/Y51S,N55G/Y51G, N55A/Y51L, N55A/Y51V, N55A/Y51A, N55A/Y51N, N55A/Y51Q,N55A/Y51S, N55A/Y51G, N55T/Y51L, N55T/Y51V, N55T/Y51A, N55T/Y51N,N55T/Y51Q, N55T/Y51S, N55T/Y51G, F56N/N55Q/Y51L, F56N/N55Q/Y51V,F56N/N55Q/Y51A, F56N/N55Q/Y51N, F56N/N55Q/Y51Q, F56N/N55Q/Y51S,F56N/N55Q/Y51G, F56N/N55R/Y51L, F56N/N55R/Y51V, F56N/N55R/Y51A,F56N/N55R/Y51N, F56N/N55R/Y51Q, F56N/N55R/Y51S, F56N/N55R/Y51G,F56N/N55K/Y51L, F56N/N55K/Y51V, F56N/N55K/Y51A, F56N/N55K/Y51N,F56N/N55K/Y51Q, F56N/N55K/Y51S, F56N/N55K/Y51G, F56N/N55S/Y51L,F56N/N55S/Y51V, F56N/N55S/Y51A, F56N/N55S/Y51N, F56N/N55S/Y51Q,F56N/N55S/Y51S, F56N/N55S/Y51G, F56N/N55G/Y51L, F56N/N55G/Y51V,F56N/N55G/Y51A, F56N/N55G/Y51N, F56N/N55G/Y51Q, F56N/N55G/Y51S,F56N/N55G/Y51G, F56N/N55A/Y51L, F56N/N55A/Y51V, F56N/N55A/Y51A,F56N/N55A/Y51N, F56N/N55A/Y51Q, F56N/N55A/Y51S, F56N/N55A/Y51G,F56N/N55T/Y51L, F56N/N55T/Y51V, F56N/N55T/Y51A, F56N/N55T/Y51N,F56N/N55T/Y51Q, F56N/N55T/Y51S, F56N/N55T/Y51G, F56Q/N55Q/Y51L,F56Q/N55Q/Y51V, F56Q/N55Q/Y51A, F56Q/N55Q/Y51N, F56Q/N55Q/Y51Q,F56Q/N55Q/Y51S, F56Q/N55Q/Y51G, F56Q/N55R/Y51L, F56Q/N55R/Y51V,F56Q/N55R/Y51A, F56Q/N55R/Y51N, F56Q/N55R/Y51Q, F56Q/N55R/Y51S,F56Q/N55R/Y51G, F56Q/N55K/Y51L, F56Q/N55K/Y51V, F56Q/N55K/Y51A,F56Q/N55K/Y51N, F56Q/N55K/Y51Q, F56Q/N55K/Y51S, F56Q/N55K/Y51G,F56Q/N55S/Y51L, F56Q/N55S/Y51V, F56Q/N55S/Y51A, F56Q/N55S/Y51N,F56Q/N55S/Y51Q, F56Q/N55S/Y51S, F56Q/N55S/Y51G, F56Q/N55G/Y51L,F56Q/N55G/Y51V, F56Q/N55G/Y51A, F56Q/N55G/Y51N, F56Q/N55G/Y51Q,F56Q/N55G/Y51S, F56Q/N55G/Y51G, F56Q/N55A/Y51L, F56Q/N55A/Y51V,F56Q/N55A/Y51A, F56Q/N55A/Y51N, F56Q/N55A/Y51Q, F56Q/N55A/Y51S,F56Q/N55A/Y51G, F56Q/N55T/Y51L, F56Q/N55T/Y51V, F56Q/N55T/Y51A,F56Q/N55T/Y51N, F56Q/N55T/Y51Q, F56Q/N55T/Y51S, F56Q/N55T/Y51G,F56R/N55Q/Y51L, F56R/N55Q/Y51V, F56R/N55Q/Y51A, F56R/N55Q/Y51N,F56R/N55Q/Y51Q, F56R/N55Q/Y51S, F56R/N55Q/Y51G, F56R/N55R/Y51L,F56R/N55R/Y51V, F56R/N55R/Y51A, F56R/N55R/Y51N, F56R/N55R/Y51Q,F56R/N55R/Y51S, F56R/N55R/Y51G, F56R/N55K/Y51L, F56R/N55K/Y51V,F56R/N55K/Y51A, F56R/N55K/Y51N, F56R/N55K/Y51Q, F56R/N55K/Y51S,F56R/N55K/Y51G, F56R/N55S/Y51L, F56R/N55S/Y51V, F56R/N55S/Y51A,F56R/N55S/Y51N, F56R/N55S/Y51Q, F56R/N55S/Y51S, F56R/N55S/Y51G,F56R/N55G/Y51L, F56R/N55G/Y51V, F56R/N55G/Y51A, F56R/N55G/Y51N,F56R/N55G/Y51Q, F56R/N55G/Y51S, F56R/N55G/Y51G, F56R/N55A/Y51L,F56R/N55A/Y51V, F56R/N55A/Y51A, F56R/N55A/Y51N, F56R/N55A/Y51Q,F56R/N55A/Y51S, F56R/N55A/Y51G, F56R/N55T/Y51L, F56R/N55T/Y51V,F56R/N55T/Y51A, F56R/N55T/Y51N, F56R/N55T/Y51Q, F56R/N55T/Y51S,F56R/N55T/Y51G, F56S/N55Q/Y51L, F56S/N55Q/Y51V, F56S/N55Q/Y51A,F56S/N55Q/Y51N, F56S/N55Q/Y51Q, F56S/N55Q/Y51S, F56S/N55Q/Y51G,F56S/N55R/Y51L, F56S/N55R/Y51V, F56S/N55R/Y51A, F56S/N55R/Y51N,F56S/N55R/Y51Q, F56S/N55R/Y51S, F56S/N55R/Y51G, F56S/N55K/Y51L,F56S/N55K/Y51V, F56S/N55K/Y51A, F56S/N55K/Y51N, F56S/N55K/Y51Q,F56S/N55K/Y51S, F56S/N55K/Y51G, F56S/N55S/Y51L, F56S/N55S/Y51V,F56S/N55S/Y51A, F56S/N55S/Y51N, F56S/N55S/Y51Q, F56S/N55S/Y51S,F56S/N55S/Y51G, F56S/N55G/Y51L, F56S/N55G/Y51V, F56S/N55G/Y51A,F56S/N55G/Y51N, F56S/N55G/Y51Q, F56S/N55G/Y51S, F56S/N55G/Y51G,F56S/N55A/Y51L, F56S/N55A/Y51V, F56S/N55A/Y51A, F56S/N55A/Y51N,F56S/N55A/Y51Q, F56S/N55A/Y51S, F56S/N55A/Y51G, F56S/N55T/Y51L,F56S/N55T/Y51V, F56S/N55T/Y51A, F56S/N55T/Y51N, F56S/N55T/Y51Q,F56S/N55T/Y51S, F56S/N55T/Y51G, F56G/N55Q/Y51L, F56G/N55Q/Y51V,F56G/N55Q/Y51A, F56G/N55Q/Y51N, F56G/N55Q/Y51Q, F56G/N55Q/Y51S,F56G/N55Q/Y51G, F56G/N55R/Y51L, F56G/N55R/Y51V, F56G/N55R/Y51A,F56G/N55R/Y51N, F56G/N55R/Y51Q, F56G/N55R/Y51S, F56G/N55R/Y51G,F56G/N55K/Y51L, F56G/N55K/Y51V, F56G/N55K/Y51A, F56G/N55K/Y51N,F56G/N55K/Y51Q, F56G/N55K/Y51S, F56G/N55K/Y51G, F56G/N55S/Y51L,F56G/N55S/Y51V, F56G/N55S/Y51A, F56G/N55S/Y51N, F56G/N55S/Y51Q,F56G/N55S/Y51S, F56G/N55S/Y51G, F56G/N55G/Y51L, F56G/N55G/Y51V,F56G/N55G/Y51A, F56G/N55G/Y51N, F56G/N55G/Y51Q, F56G/N55G/Y51S,F56G/N55G/Y51G, F56G/N55A/Y51L, F56G/N55A/Y51V, F56G/N55A/Y51A,F56G/N55A/Y51N, F56G/N55A/Y51Q, F56G/N55A/Y51S, F56G/N55A/Y51G,F56G/N55T/Y51L, F56G/N55T/Y51V, F56G/N55T/Y51A, F56G/N55T/Y51N,F56G/N55T/Y51Q, F56G/N55T/Y51S, F56G/N55T/Y51G, F56A/N55Q/Y51L,F56A/N55Q/Y51V, F56A/N55Q/Y51A, F56A/N55Q/Y51N, F56A/N55Q/Y51Q,F56A/N55Q/Y51S, F56A/N55Q/Y51G, F56A/N55R/Y51L, F56A/N55R/Y51V,F56A/N55R/Y51A, F56A/N55R/Y51N, F56A/N55R/Y51Q, F56A/N55R/Y51S,F56A/N55R/Y51G, F56A/N55K/Y51L, F56A/N55K/Y51V, F56A/N55K/Y51A,F56A/N55K/Y51N, F56A/N55K/Y51Q, F56A/N55K/Y51S, F56A/N55K/Y51G,F56A/N55S/Y51L, F56A/N55S/Y51V, F56A/N55S/Y51A, F56A/N55S/Y51N,F56A/N55S/Y51Q, F56A/N55S/Y51S, F56A/N55S/Y51G, F56A/N55G/Y51L,F56A/N55G/Y51V, F56A/N55G/Y51A, F56A/N55G/Y51N, F56A/N55G/Y51Q,F56A/N55G/Y51S, F56A/N55G/Y51G, F56A/N55A/Y51L, F56A/N55A/Y51V,F56A/N55A/Y51A, F56A/N55A/Y51N, F56A/N55A/Y51Q, F56A/N55A/Y51S,F56A/N55A/Y51G, F56A/N55T/Y51L, F56A/N55T/Y51V, F56A/N55T/Y51A,F56A/N55T/Y51N, F56A/N55T/Y51Q, F56A/N55T/Y51S, F56A/N55T/Y51G,F56K/N55Q/Y51L, F56K/N55Q/Y51V, F56K/N55Q/Y51A, F56K/N55Q/Y51N,F56K/N55Q/Y51Q, F56K/N55Q/Y51S, F56K/N55Q/Y51G, F56K/N55R/Y51L,F56K/N55R/Y51V, F56K/N55R/Y51A, F56K/N55R/Y51N, F56K/N55R/Y51Q,F56K/N55R/Y51S, F56K/N55R/Y51G, F56K/N55K/Y51L, F56K/N55K/Y51V,F56K/N55K/Y51A, F56K/N55K/Y51N, F56K/N55K/Y51Q, F56K/N55K/Y51S,F56K/N55K/Y51G, F56K/N55S/Y51L, F56K/N55S/Y51V, F56K/N55S/Y51A,F56K/N55S/Y51N, F56K/N55S/Y51Q, F56K/N55S/Y51S, F56K/N55S/Y51G,F56K/N55G/Y51L, F56K/N55G/Y51V, F56K/N55G/Y51A, F56K/N55G/Y51N,F56K/N55G/Y51Q, F56K/N55G/Y51S, F56K/N55G/Y51G, F56K/N55A/Y51L,F56K/N55A/Y51V, F56K/N55A/Y51A, F56K/N55A/Y51N, F56K/N55A/Y51Q,F56K/N55A/Y51S, F56K/N55A/Y51G, F56K/N55T/Y51L, F56K/N55T/Y51V,F56K/N55T/Y51A, F56K/N55T/Y51N, F56K/N55T/Y51Q, F56K/N55T/Y51S,F56K/N55T/Y51G, F56E/N55R, F56E/N55K, F56D/N55R, F56D/N55K, F56R/N55E,F56R/N55D, F56K/N55E or F56K/N55D; and/or (c) the variant comprisesdeletion of Y51/P52, Y51/P52/A53, P50 to P52, P50 to A53, K49 to Y51,K49 to A53 and replacement with a single proline (P), K49 to S54 andreplacement with a single P, Y51 to A53, Y51 to S54, N55/F56, N55 toS57, N55/F56 and replacement with a single P, N55/F56 and replacementwith a single glycine (G), N55/F56 and replacement with a single alanine(A), N55/F56 and replacement with a single P and Y51N, N55/F56 andreplacement with a single P and Y51Q, N55/F56 and replacement with asingle P and Y51S, N55/F56 and replacement with a single G and Y51N,N55/F56 and replacement with a single G and Y51Q, N55/F56 andreplacement with a single G and Y51S, N55/F56 and replacement with asingle A and Y51N, N55/F56 and replacement with a single A/Y51Q orN55/F56 and replacement with a single A and Y51S.
 7. A mutant accordingto claim 1, wherein the variant comprises D195N/E203N, D195Q/E203N,D195N/E203Q, D195Q/E203Q, E201N/E203N, E201Q/E203N, E201N/E203Q,E201Q/E203Q, E185N/E203Q, E185Q/E203Q, E185N/E203N, E185Q/E203N,D195N/E201N/E203N, D195Q/E201N/E203N, D195N/E201Q/E203N,D195N/E201N/E203Q, D195Q/E201Q/E203N, D195Q/E201N/E203Q,D195N/E201Q/E203Q, D195Q/E201Q/E203Q, D149N/E201N, D149Q/E201N,D149N/E201Q, D149Q/E201Q, D149N/E201N/D195N, D149Q/E201N/D195N,D149N/E201Q/D195N, D149N/E201N/D195Q, D149Q/E201Q/D195N,D149Q/E201N/D195Q, D149N/E201Q/D195Q, D149Q/E201Q/D195Q, D149N/E203N,D149Q/E203N, D149N/E203Q, D149Q/E203Q, D149N/E185N/E201N,D149Q/E185N/E201N, D149N/E185Q/E201N, D149N/E185N/E201Q,D149Q/E185Q/E201N, D149Q/E185N/E201Q, D149N/E185Q/E201Q,D149Q/E185Q/E201Q, D149N/E185N/E203N, D149Q/E185N/E203N,D149N/E185Q/E203N, D149N/E185N/E203Q, D149Q/E185Q/E203N,D149Q/E185N/E203Q, D149N/E185Q/E203Q, D149Q/E185Q/E203Q,D149N/E185N/E201N/E203N, D149Q/E185N/E201N/E203N,D149N/E185Q/E201N/E203N, D149N/E185N/E201Q/E203N,D149N/E185N/E201N/E203Q, D149Q/E185Q/E201N/E203N,D149Q/E185N/E201Q/E203N, D149Q/E185N/E201N/E203Q,D149N/E185Q/E201Q/E203N, D149N/E185Q/E201N/E203Q,D149N/E185N/E201Q/E203Q, D149Q/E185Q/E201Q/E203Q,D149Q/E185Q/E201N/E203Q, D149Q/E185N/E201Q/E203Q,D149N/E185Q/E201Q/E203Q, D149Q/E185Q/E201Q/E203N,D149N/E185N/D195N/E201N/E203N, D149Q/E185N/D195N/E201N/E203N,D149N/E185Q/D195N/E201N/E203N, D149N/E185N/D195Q/E201N/E203N,D149N/E185N/D195N/E201Q/E203N, D149N/E185N/D195N/E201N/E203Q,D149Q/E185Q/D195N/E201N/E203N, D149Q/E185N/D195Q/E201N/E203N,D149Q/E185N/D195N/E201Q/E203N, D149Q/E185N/D195N/E201N/E203Q,D149N/E185Q/D195Q/E201N/E203N, D149N/E185Q/D195N/E201Q/E203N,D149N/E185Q/D195N/E201N/E203Q, D149N/E185N/D195Q/E201Q/E203N,D149N/E185N/D195Q/E201N/E203Q, D149N/E185N/D195N/E201Q/E203Q,D149Q/E185Q/D195Q/E201N/E203N, D149Q/E185Q/D195N/E201Q/E203N,D149Q/E185Q/D195N/E201N/E203Q, D149Q/E185N/D195Q/E201Q/E203N,D149Q/E185N/D195Q/E201N/E203Q, D149Q/E185N/D195N/E201Q/E203Q,D149N/E185Q/D195Q/E201Q/E203N, D149N/E185Q/D195Q/E201N/E203Q,D149N/E185Q/D195N/E201Q/E203Q, D149N/E185N/D195Q/E201Q/E203Q,D149Q/E185Q/D195Q/E201Q/E203N, D149Q/E185Q/D195Q/E201N/E203Q,D149Q/E185Q/D195N/E201Q/E203Q, D149Q/E185N/D195Q/E201Q/E203Q,D149N/E185Q/D195Q/E201Q/E203Q, D149Q/E185Q/D195Q/E201Q/E203Q,D149N/E185R/E201N/E203N, D149Q/E185R/E201N/E203N,D149N/E185R/E201Q/E203N, D149N/E185R/E201N/E203Q,D149Q/E185R/E201Q/E203N, D149Q/E185R/E201N/E203Q,D149N/E185R/E201Q/E203Q, D149Q/E185R/E201Q/E203Q,D149R/E185N/E201N/E203N, D149R/E185Q/E201N/E203N,D149R/E185N/E201Q/E203N, D149R/E185N/E201N/E203Q,D149R/E185Q/E201Q/E203N, D149R/E185Q/E201N/E203Q,D149R/E185N/E201Q/E203Q, D149R/E185Q/E201Q/E203Q,D149R/E185N/D195N/E201N/E203N, D149R/E185Q/D195N/E201N/E203N,D149R/E185N/D195Q/E201N/E203N, D149R/E185N/D195N/E201Q/E203N,D149R/E185Q/D195N/E201N/E203Q, D149R/E185Q/D195Q/E201N/E203N,D149R/E185Q/D195N/E201Q/E203N, D149R/E185Q/D195N/E201N/E203Q,D149R/E185N/D195Q/E201Q/E203N, D149R/E185N/D195Q/E201N/E203Q,D149R/E185N/D195N/E201Q/E203Q, D149R/E185Q/D195Q/E201Q/E203N,D149R/E185Q/D195Q/E201N/E203Q, D149R/E185Q/D195N/E201Q/E203Q,D149R/E185N/D195Q/E201Q/E203Q, D149R/E185Q/D195Q/E201Q/E203Q,D149N/E185R/D195N/E201N/E203N, D149Q/E185R/D195N/E201N/E203N,D149N/E185R/D195Q/E201N/E203N, D149N/E185R/D195N/E201Q/E203N,D149N/E185R/D195N/E201N/E203Q, D149Q/E185R/D195Q/E201N/E203N,D149Q/E185R/D195N/E201Q/E203N, D149Q/E185R/D195N/E201N/E203Q,D149N/E185R/D195Q/E201Q/E203N, D149N/E185R/D195Q/E201N/E203Q,D149N/E185R/D195N/E201Q/E203Q, D149Q/E185R/D195Q/E201Q/E203N,D149Q/E185R/D195Q/E201N/E203Q, D149Q/E185R/D195N/E201Q/E203Q,D149N/E185R/D195Q/E201Q/E203Q, D149Q/E185R/D195Q/E201Q/E203Q,D149N/E185R/D195N/E201R/E203N, D149Q/E185R/D195N/E201R/E203N,D149N/E185R/D195Q/E201R/E203N, D149N/E185R/D195N/E201R/E203Q,D149Q/E185R/D195Q/E201R/E203N, D149Q/E185R/D195N/E201R/E203Q,D149N/E185R/D195Q/E201R/E203Q, D149Q/E185R/D195Q/E201R/E203Q,E131D/K49R, E101N/N102F, E101N/N102Y, E101N/N102W, E101F/N102F,E101F/N102Y, E101F/N102W, E101Y/N102F, E101Y/N102Y, E101Y/N102W,E101W/N102F, E101W/N102Y, E101W/N102W, E101N/N102R, E101F/N102R,E101Y/N102R or E101W/N102F.
 8. A mutant monomer according to claim 1,wherein the variant comprises a mutation at T150.
 9. A constructcomprising two or more covalently attached CsgG monomers, wherein atleast one of the monomers is a mutant monomer according to claim
 1. 10.A construct according to claim 9, wherein the two or more mutantmonomers are the same or different.
 11. A construct according to claim9, wherein the two or more mutant monomers are genetically fused.
 12. Aconstruct according to claim 9, wherein the two or more mutant monomersare attached via one or more linkers.
 13. A construct according to claim9, wherein the construct comprises two mutant monomers.
 14. Apolynucleotide which encodes a mutant monomer according to claim
 1. 15.A homo-oligomeric pore derived from CsgG comprising identical mutantmonomers according to claim 1 or identical constructs.
 16. Ahomo-oligomeric pore according to claim 15, wherein the pore comprisesnine identical mutant monomers.
 17. A hetero-oligomeric pore derivedfrom CsgG comprising at least one mutant monomer according to claim 1 orat least one construct.
 18. A hetero-oligomeric pore according to claim17, wherein the pore comprises (a) nine mutant monomers and wherein atleast one of them differs from the others or (b) one or more mutantmonomers and sufficient additional monomers comprising SEQ ID NO:
 2. 19.A method for determining the presence, absence or one or morecharacteristics of a target analyte, comprising: (a) contacting thetarget analyte with a pore according to claim 15 such that the targetanalyte moves with respect to the pore; and (b) taking one or moremeasurements as the analyte moves with respect to the pore and therebydetermining the presence, absence or one or more characteristics of theanalyte. 20.-46. (canceled)